A comparison of parsing technologies for the biomedical domain

This paper reports on a number of experiments which are designed to investigate the extent to which current nlp resources are able to syntactically and semantically analyse biomedical text. We address two tasks: parsing a real corpus with a hand-built widecoverage grammar, producing both syntactic analyses and logical forms; and automatically computing the interpretation of compound nouns where the head is a nominalisation (e.g., hospital arrival means an arrival at hospital, while patient arrival means an arrival of a patient). For the former task we demonstrate that exible and yet constrained `preprocessing ' techniques are crucial to success: these enable us to use part-of-speech tags to overcome inadequate lexical coverage, and to `package up' complex technical expressions prior to parsing so that they are blocked from creating misleading amounts of syntactic complexity. We argue that the xml-processing paradigm is ideally suited for automatically preparing the corpus for parsing. For the latter task, we compute interpretations of the compounds by exploiting surface cues and meaning paraphrases, which in turn are extracted from the parsed corpus. This provides an empirical setting in which we can compare the utility of a comparatively deep parser vs. a shallow one, exploring the trade-o between resolving attachment ambiguities on the one hand and generating errors in the parses on the other. We demonstrate that a model of the meaning of compound nominalisations is achievable with the aid of current broad-coverage parsers

Multi modal multi-semantic image retrieval

PhDThe rapid growth in the volume of visual information, e.g. image, and video can overwhelm users’ ability to find and access the specific visual information of interest to them. In recent years, ontology knowledge-based (KB) image information retrieval techniques have been adopted into in order to attempt to extract knowledge from these images, enhancing the retrieval performance. A KB framework is presented to promote semi-automatic annotation and semantic image retrieval using multimodal cues (visual features and text captions). In addition, a hierarchical structure for the KB allows metadata to be shared that supports multi-semantics (polysemy) for concepts. The framework builds up an effective knowledge base pertaining to a domain specific image collection, e.g. sports, and is able to disambiguate and assign high level semantics to ‘unannotated’ images. Local feature analysis of visual content, namely using Scale Invariant Feature Transform (SIFT) descriptors, have been deployed in the ‘Bag of Visual Words’ model (BVW) as an effective method to represent visual content information and to enhance its classification and retrieval. Local features are more useful than global features, e.g. colour, shape or texture, as they are invariant to image scale, orientation and camera angle. An innovative approach is proposed for the representation, annotation and retrieval of visual content using a hybrid technique based upon the use of an unstructured visual word and upon a (structured) hierarchical ontology KB model. The structural model facilitates the disambiguation of unstructured visual words and a more effective classification of visual content, compared to a vector space model, through exploiting local conceptual structures and their relationships. The key contributions of this framework in using local features for image representation include: first, a method to generate visual words using the semantic local adaptive clustering (SLAC) algorithm which takes term weight and spatial locations of keypoints into account. Consequently, the semantic information is preserved. Second a technique is used to detect the domain specific ‘non-informative visual words’ which are ineffective at representing the content of visual data and degrade its categorisation ability. Third, a method to combine an ontology model with xi a visual word model to resolve synonym (visual heterogeneity) and polysemy problems, is proposed. The experimental results show that this approach can discover semantically meaningful visual content descriptions and recognise specific events, e.g., sports events, depicted in images efficiently. Since discovering the semantics of an image is an extremely challenging problem, one promising approach to enhance visual content interpretation is to use any associated textual information that accompanies an image, as a cue to predict the meaning of an image, by transforming this textual information into a structured annotation for an image e.g. using XML, RDF, OWL or MPEG-7. Although, text and image are distinct types of information representation and modality, there are some strong, invariant, implicit, connections between images and any accompanying text information. Semantic analysis of image captions can be used by image retrieval systems to retrieve selected images more precisely. To do this, a Natural Language Processing (NLP) is exploited firstly in order to extract concepts from image captions. Next, an ontology-based knowledge model is deployed in order to resolve natural language ambiguities. To deal with the accompanying text information, two methods to extract knowledge from textual information have been proposed. First, metadata can be extracted automatically from text captions and restructured with respect to a semantic model. Second, the use of LSI in relation to a domain-specific ontology-based knowledge model enables the combined framework to tolerate ambiguities and variations (incompleteness) of metadata. The use of the ontology-based knowledge model allows the system to find indirectly relevant concepts in image captions and thus leverage these to represent the semantics of images at a higher level. Experimental results show that the proposed framework significantly enhances image retrieval and leads to narrowing of the semantic gap between lower level machinederived and higher level human-understandable conceptualisation

An Urdu semantic tagger - lexicons, corpora, methods and tools

Extracting and analysing meaning-related information from natural language data has attracted the attention of researchers in various fields, such as Natural Language Processing (NLP), corpus linguistics, data sciences, etc. An important aspect of such automatic information extraction and analysis is the semantic annotation of language data using semantic annotation tool (a.k.a semantic tagger). Generally, different semantic annotation tools have been designed to carry out various levels of semantic annotations, for instance, sentiment analysis, word sense disambiguation, content analysis, semantic role labelling, etc. These semantic annotation tools identify or tag partial core semantic information of language data, moreover, they tend to be applicable only for English and other European languages. A semantic annotation tool that can annotate semantic senses of all lexical units (words) is still desirable for the Urdu language based on USAS (the UCREL Semantic Analysis System) semantic taxonomy, in order to provide comprehensive semantic analysis of Urdu language text. This research work report on the development of an Urdu semantic tagging tool and discuss challenging issues which have been faced in this Ph.D. research work. Since standard NLP pipeline tools are not widely available for Urdu, alongside the Urdu semantic tagger a suite of newly developed tools have been created: sentence tokenizer, word tokenizer and part-of-speech tagger. Results for these proposed tools are as follows: word tokenizer reports $F_1$ of 94.01\%, and accuracy of 97.21\%, sentence tokenizer shows F$_1$ of 92.59\%, and accuracy of 93.15\%, whereas, POS tagger shows an accuracy of 95.14\%. The Urdu semantic tagger incorporates semantic resources (lexicon and corpora) as well as semantic field disambiguation methods. In terms of novelty, the NLP pre-processing tools are developed either using rule-based, statistical, or hybrid techniques. Furthermore, all semantic lexicons have been developed using a novel combination of automatic or semi-automatic approaches: mapping, crowdsourcing, statistical machine translation, GIZA++, word embeddings, and named entity. A large multi-target annotated corpus is also constructed using a semi-automatic approach to test accuracy of the Urdu semantic tagger, proposed corpus is also used to train and test supervised multi-target Machine Learning classifiers. The results show that Random k-labEL Disjoint Pruned Sets and Classifier Chain multi-target classifiers outperform all other classifiers on the proposed corpus with a Hamming Loss of 0.06\% and Accuracy of 0.94\%. The best lexical coverage of 88.59\%, 99.63\%, 96.71\% and 89.63\% are obtained on several test corpora. The developed Urdu semantic tagger shows encouraging precision on the proposed test corpus of 79.47\%

A Biased Topic Modeling Approach for Case Control Study from Health Related Social Media Postings

abstract: Online social networks are the hubs of social activity in cyberspace, and using them to exchange knowledge, experiences, and opinions is common. In this work, an advanced topic modeling framework is designed to analyse complex longitudinal health information from social media with minimal human annotation, and Adverse Drug Events and Reaction (ADR) information is extracted and automatically processed by using a biased topic modeling method. This framework improves and extends existing topic modelling algorithms that incorporate background knowledge. Using this approach, background knowledge such as ADR terms and other biomedical knowledge can be incorporated during the text mining process, with scores which indicate the presence of ADR being generated. A case control study has been performed on a data set of twitter timelines of women that announced their pregnancy, the goals of the study is to compare the ADR risk of medication usage from each medication category during the pregnancy. In addition, to evaluate the prediction power of this approach, another important aspect of personalized medicine was addressed: the prediction of medication usage through the identification of risk groups. During the prediction process, the health information from Twitter timeline, such as diseases, symptoms, treatments, effects, and etc., is summarized by the topic modelling processes and the summarization results is used for prediction. Dimension reduction and topic similarity measurement are integrated into this framework for timeline classification and prediction. This work could be applied to provide guidelines for FDA drug risk categories. Currently, this process is done based on laboratory results and reported cases. Finally, a multi-dimensional text data warehouse (MTD) to manage the output from the topic modelling is proposed. Some attempts have been also made to incorporate topic structure (ontology) and the MTD hierarchy. Results demonstrate that proposed methods show promise and this system represents a low-cost approach for drug safety early warning.Dissertation/ThesisDoctoral Dissertation Computer Science 201

Proceedings of the COLING 2004 Post Conference Workshop on Multilingual Linguistic Ressources MLR2004

International audienceIn an ever expanding information society, most information systems are now facing the "multilingual challenge". Multilingual language resources play an essential role in modern information systems. Such resources need to provide information on many languages in a common framework and should be (re)usable in many applications (for automatic or human use). Many centres have been involved in national and international projects dedicated to building har- monised language resources and creating expertise in the maintenance and further development of standardised linguistic data. These resources include dictionaries, lexicons, thesauri, word-nets, and annotated corpora developed along the lines of best practices and recommendations. However, since the late 90's, most efforts in scaling up these resources remain the responsibility of the local authorities, usually, with very low funding (if any) and few opportunities for academic recognition of this work. Hence, it is not surprising that many of the resource holders and developers have become reluctant to give free access to the latest versions of their resources, and their actual status is therefore currently rather unclear. The goal of this workshop is to study problems involved in the development, management and reuse of lexical resources in a multilingual context. Moreover, this workshop provides a forum for reviewing the present state of language resources. The workshop is meant to bring to the international community qualitative and quantitative information about the most recent developments in the area of linguistic resources and their use in applications. The impressive number of submissions (38) to this workshop and in other workshops and conferences dedicated to similar topics proves that dealing with multilingual linguistic ressources has become a very hot problem in the Natural Language Processing community. To cope with the number of submissions, the workshop organising committee decided to accept 16 papers from 10 countries based on the reviewers' recommendations. Six of these papers will be presented in a poster session. The papers constitute a representative selection of current trends in research on Multilingual Language Resources, such as multilingual aligned corpora, bilingual and multilingual lexicons, and multilingual speech resources. The papers also represent a characteristic set of approaches to the development of multilingual language resources, such as automatic extraction of information from corpora, combination and re-use of existing resources, online collaborative development of multilingual lexicons, and use of the Web as a multilingual language resource. The development and management of multilingual language resources is a long-term activity in which collaboration among researchers is essential. We hope that this workshop will gather many researchers involved in such developments and will give them the opportunity to discuss, exchange, compare their approaches and strengthen their collaborations in the field. The organisation of this workshop would have been impossible without the hard work of the program committee who managed to provide accurate reviews on time, on a rather tight schedule. We would also like to thank the Coling 2004 organising committee that made this workshop possible. Finally, we hope that this workshop will yield fruitful results for all participants

Semantic Relevance Analysis of Subject-Predicate-Object (SPO) Triples

The goal of this thesis is to explore and integrate several existing measurements for ranking the relevance of a set of subject-predicate-object (SPO) triples to a given concept. As we are inundated with information from multiple sources on the World-Wide-Web, SPO similarity measures play a progressively important role in information extraction, information retrieval, document clustering and ontology learning. This thesis is applied in the Cyber Security Domain for identifying and understanding the factors and elements of sociopolitical events relevant to cyberattacks. Our efforts are towards developing an algorithm that begins with an analysis of news articles by taking into account the semantic information and word order information in the SPOs extracted from the articles. The semantic cohesiveness of a user provided concept and the extracted SPOs will then be calculated using semantic similarity measures derived from 1) structured lexical databases; and 2) our own corpus statistics. The use of a lexical database will enable our method to model human common sense knowledge, while the incorporation of our own corpus statistics allows our method to be adaptable to the Cyber Security domain. The model can be extended to other domains by simply changing the local corpus. The integration of different measures will help us triangulate the ranking of SPOs from multiple dimensions of semantic cohesiveness. Our results are compared to rankings gathered from surveys of human users, where each respondent ranks a list of SPO based on their common knowledge and understanding of the relevance evaluations to a given concept. The comparison demonstrates that our integrated SPO similarity ranking scheme closely reflects the human common sense knowledge in a specific domain it addresses

Verb Semantics for English-Chinese Translation

A common practice in operational Machine Translation (MT) and Natural Language Processing (NLP) systems is to assume that a verb has a fixed number of senses and rely on a precompiled lexicon to achieve large coverage. This paper demonstrates that this assumption is too weak to cope with the similar problems of lexical divergences between languages and unexpected uses of words that give rise to cases outside of the precompiled lexicon coverage. We first examine the lexical divergences between English verbs and Chinese verbs. We then focus on a specic lexical selection problem - translating English change-of-state verbs into Chinese verb compounds. We show that an accurate translation depends not only on information about the participants, but also on contextual information. Therefore, selectional restrictions on verb arguments lack the necessary power for accurate lexical selection. Second, we examine verb representation theories and practices in MT systems and show that under the fixed sense assumption, the existing representation schemes are not adequate for handling these lexical divergences and extending existing verb senses to unexpected usages. We then propose a method of verb representation based on conceptual lattices which allows the similarities among different verbs in different languages to be quantitatively measured. A prototype system UNICON implements this theory and performs more accurate MT lexical selection for our chosen set of verbs. An additional lexical module for UNICON is also provided that handles sense extension

Automatic Population of Structured Reports from Narrative Pathology Reports

There are a number of advantages for the use of structured pathology reports: they can ensure the accuracy and completeness of pathology reporting; it is easier for the referring doctors to glean pertinent information from them. The goal of this thesis is to extract pertinent information from free-text pathology reports and automatically populate structured reports for cancer diseases and identify the commonalities and differences in processing principles to obtain maximum accuracy. Three pathology corpora were annotated with entities and relationships between the entities in this study, namely the melanoma corpus, the colorectal cancer corpus and the lymphoma corpus. A supervised machine-learning based-approach, utilising conditional random fields learners, was developed to recognise medical entities from the corpora. By feature engineering, the best feature configurations were attained, which boosted the F-scores significantly from 4.2% to 6.8% on the training sets. Without proper negation and uncertainty detection, the quality of the structured reports will be diminished. The negation and uncertainty detection modules were built to handle this problem. The modules obtained overall F-scores ranging from 76.6% to 91.0% on the test sets. A relation extraction system was presented to extract four relations from the lymphoma corpus. The system achieved very good performance on the training set, with 100% F-score obtained by the rule-based module and 97.2% F-score attained by the support vector machines classifier. Rule-based approaches were used to generate the structured outputs and populate them to predefined templates. The rule-based system attained over 97% F-scores on the training sets. A pipeline system was implemented with an assembly of all the components described above. It achieved promising results in the end-to-end evaluations, with 86.5%, 84.2% and 78.9% F-scores on the melanoma, colorectal cancer and lymphoma test sets respectively

Three Essays on Enhancing Clinical Trial Subject Recruitment Using Natural Language Processing and Text Mining

Patient recruitment and enrollment are critical factors for a successful clinical trial; however, recruitment tends to be the most common problem in most clinical trials. The success of a clinical trial depends on efficiently recruiting suitable patients to conduct the trial. Every clinical trial research has a protocol, which describes what will be done in the study and how it will be conducted. Also, the protocol ensures the safety of the trial subjects and the integrity of the data collected. The eligibility criteria section of clinical trial protocols is important because it specifies the necessary conditions that participants have to satisfy. Since clinical trial eligibility criteria are usually written in free text form, they are not computer interpretable. To automate the analysis of the eligibility criteria, it is therefore necessary to transform those criteria into a computer-interpretable format. Unstructured format of eligibility criteria additionally create search efficiency issues. Thus, searching and selecting appropriate clinical trials for a patient from relatively large number of available trials is a complex task. A few attempts have been made to automate the matching process between patients and clinical trials. However, those attempts have not fully integrated the entire matching process and have not exploited the state-of-the-art Natural Language Processing (NLP) techniques that may improve the matching performance. Given the importance of patient recruitment in clinical trial research, the objective of this research is to automate the matching process using NLP and text mining techniques and, thereby, improve the efficiency and effectiveness of the recruitment process. This dissertation research, which comprises three essays, investigates the issues of clinical trial subject recruitment using state-of-the-art NLP and text mining techniques. Essay 1: Building a Domain-Specific Lexicon for Clinical Trial Subject Eligibility Analysis Essay 2: Clustering Clinical Trials Using Semantic-Based Feature Expansion Essay 3: An Automatic Matching Process of Clinical Trial Subject Recruitment In essay1, I develop a domain-specific lexicon for n-gram Named Entity Recognition (NER) in the breast cancer domain. The domain-specific dictionary is used for selection and reduction of n-gram features in clustering in eassy2. The domain-specific dictionary was evaluated by comparing it with Systematized Nomenclature of Medicine--Clinical Terms (SNOMED CT). The results showed that it add significant number of new terms which is very useful in effective natural language processing In essay 2, I explore the clustering of similar clinical trials using the domain-specific lexicon and term expansion using synonym from the Unified Medical Language System (UMLS). I generate word n-gram features and modify the features with the domain-specific dictionary matching process. In order to resolve semantic ambiguity, a semantic-based feature expansion technique using UMLS is applied. A hierarchical agglomerative clustering algorithm is used to generate clinical trial clusters. The focus is on summarization of clinical trial information in order to enhance trial search efficiency. Finally, in essay 3, I investigate an automatic matching process of clinical trial clusters and patient medical records. The patient records collected from a prior study were used to test our approach. The patient records were pre-processed by tokenization and lemmatization. The pre-processed patient information were then further enhanced by matching with breast cancer custom dictionary described in essay 1 and semantic feature expansion using UMLS Metathesaurus. Finally, I matched the patient record with clinical trial clusters to select the best matched cluster(s) and then with trials within the clusters. The matching results were evaluated by internal expert as well as external medical expert

Adaptive content mapping for internet navigation

The Internet as the biggest human library ever assembled keeps on growing. Although all kinds of information carriers (e.g. audio/video/hybrid file formats) are available, text based documents dominate. It is estimated that about 80% of all information worldwide stored electronically exists in (or can be converted into) text form. More and more, all kinds of documents are generated by means of a text processing system and are therefore available electronically. Nowadays, many printed journals are also published online and may even discontinue to appear in print form tomorrow. This development has many convincing advantages: the documents are both available faster (cf. prepress services) and cheaper, they can be searched more easily, the physical storage only needs a fraction of the space previously necessary and the medium will not age. For most people, fast and easy access is the most interesting feature of the new age; computer-aided search for specific documents or Web pages becomes the basic tool for information-oriented work. But this tool has problems. The current keyword based search machines available on the Internet are not really appropriate for such a task; either there are (way) too many documents matching the specified keywords are presented or none at all. The problem lies in the fact that it is often very difficult to choose appropriate terms describing the desired topic in the first place. This contribution discusses the current state-of-the-art techniques in content-based searching (along with common visualization/browsing approaches) and proposes a particular adaptive solution for intuitive Internet document navigation, which not only enables the user to provide full texts instead of manually selected keywords (if available), but also allows him/her to explore the whole database