Protein-protein interaction: A supervised learning approach

Master'sMASTER OF SCIENC

Large Scale Data Analytics with Language Integrated Query

Databases can easily reach petabytes (1,048,576 gigabytes) in scale. A system to enable users to efficiently retrieve or query data from multiple databases simultaneously is needed. This research introduces a new, cloud-based query framework, designed and built using Language Integrated Query, to query existing data sources without the need to integrate or restructure existing databases. Protein data obtained through the query framework proves its feasibility and cost effectiveness

Semi-Supervised Named Entity Recognition:\ud Learning to Recognize 100 Entity Types with Little Supervision\ud

Named Entity Recognition (NER) aims to extract and to classify rigid designators in text such as proper names, biological species, and temporal expressions. There has been growing interest in this field of research since the early 1990s. In this thesis, we document a trend moving away from handcrafted rules, and towards machine learning approaches. Still, recent machine learning approaches have a problem with annotated data availability, which is a serious shortcoming in building and maintaining large-scale NER systems. \ud \ud In this thesis, we present an NER system built with very little supervision. Human supervision is indeed limited to listing a few examples of each named entity (NE) type. First, we introduce a proof-of-concept semi-supervised system that can recognize four NE types. Then, we expand its capacities by improving key technologies, and we apply the system to an entire hierarchy comprised of 100 NE types. \ud \ud Our work makes the following contributions: the creation of a proof-of-concept semi-supervised NER system; the demonstration of an innovative noise filtering technique for generating NE lists; the validation of a strategy for learning disambiguation rules using automatically identified, unambiguous NEs; and finally, the development of an acronym detection algorithm, thus solving a rare but very difficult problem in alias resolution. \ud \ud We believe semi-supervised learning techniques are about to break new ground in the machine learning community. In this thesis, we show that limited supervision can build complete NER systems. On standard evaluation corpora, we report performances that compare to baseline supervised systems in the task of annotating NEs in texts. \u

Supervised classification and mathematical optimization

Data Mining techniques often ask for the resolution of optimization problems. Supervised Classification, and, in particular, Support Vector Machines, can be seen as a paradigmatic instance. In this paper, some links between Mathematical Optimization methods and Supervised Classification are emphasized. It is shown that many different areas of Mathematical Optimization play a central role in off-the-shelf Supervised Classification methods. Moreover, Mathematical Optimization turns out to be extremely useful to address important issues in Classification, such as identifying relevant variables, improving the interpretability of classifiers or dealing with vagueness/noise in the data.Ministerio de Ciencia e InnovaciónJunta de Andalucí

Investigations into the value of labeled and unlabeled data in biomedical entity recognition and word sense disambiguation

Human annotations, especially in highly technical domains, are expensive and time consuming togather, and can also be erroneous. As a result, we never have sufficiently accurate data to train andevaluate supervised methods. In this thesis, we address this problem by taking a semi-supervised approach to biomedical namedentity recognition (NER), and by proposing an inventory-independent evaluation framework for supervised and unsupervised word sense disambiguation. Our contributions are as follows: We introduce a novel graph-based semi-supervised approach to named entity recognition(NER) and exploit pre-trained contextualized word embeddings in several biomedical NER tasks. We propose a new evaluation framework for word sense disambiguation that permits a fair comparison between supervised methods trained on different sense inventories as well as unsupervised methods without a fixed sense inventory

Supervised Classification and Mathematical Optimization

Data Mining techniques often ask for the resolution of optimization problems. Supervised Classification, and, in particular, Support Vector Machines, can be seen as a paradigmatic instance. In this paper, some links between Mathematical Optimization methods and Supervised Classification are emphasized. It is shown that many different areas of Mathematical Optimization play a central role in off-the-shelf Supervised Classification methods. Moreover, Mathematical Optimization turns out to be extremely useful to address important issues in Classification, such as identifying relevant variables, improving the interpretability of classifiers or dealing with vagueness/noise in the data

Information Extraction from Text for Improving Research on Small Molecules and Histone Modifications

The cumulative number of publications, in particular in the life sciences, requires efficient methods for the automated extraction of information and semantic information retrieval. The recognition and identification of information-carrying units in text – concept denominations and named entities – relevant to a certain domain is a fundamental step. The focus of this thesis lies on the recognition of chemical entities and the new biological named entity type histone modifications, which are both important in the field of drug discovery. As the emergence of new research fields as well as the discovery and generation of novel entities goes along with the coinage of new terms, the perpetual adaptation of respective named entity recognition approaches to new domains is an important step for information extraction. Two methodologies have been investigated in this concern: the state-of-the-art machine learning method, Conditional Random Fields (CRF), and an approximate string search method based on dictionaries. Recognition methods that rely on dictionaries are strongly dependent on the availability of entity terminology collections as well as on its quality. In the case of chemical entities the terminology is distributed over more than 7 publicly available data sources. The join of entries and accompanied terminology from selected resources enables the generation of a new dictionary comprising chemical named entities. Combined with the automatic processing of respective terminology – the dictionary curation – the recognition performance reached an F1 measure of 0.54. That is an improvement by 29 % in comparison to the raw dictionary. The highest recall was achieved for the class of TRIVIAL-names with 0.79. The recognition and identification of chemical named entities provides a prerequisite for the extraction of related pharmacological relevant information from literature data. Therefore, lexico-syntactic patterns were defined that support the automated extraction of hypernymic phrases comprising pharmacological function terminology related to chemical compounds. It was shown that 29-50 % of the automatically extracted terms can be proposed for novel functional annotation of chemical entities provided by the reference database DrugBank. Furthermore, they are a basis for building up concept hierarchies and ontologies or for extending existing ones. Successively, the pharmacological function and biological activity concepts obtained from text were included into a novel descriptor for chemical compounds. Its successful application for the prediction of pharmacological function of molecules and the extension of chemical classification schemes, such as the the Anatomical Therapeutic Chemical (ATC), is demonstrated. In contrast to chemical entities, no comprehensive terminology resource has been available for histone modifications. Thus, histone modification concept terminology was primary recognized in text via CRFs with a F1 measure of 0.86. Subsequent, linguistic variants of extracted histone modification terms were mapped to standard representations that were organized into a newly assembled histone modification hierarchy. The mapping was accomplished by a novel developed term mapping approach described in the thesis. The combination of term recognition and term variant resolution builds up a new procedure for the assembly of novel terminology collections. It supports the generation of a term list that is applicable in dictionary-based methods. For the recognition of histone modification in text it could be shown that the named entity recognition method based on dictionaries is superior to the used machine learning approach. In conclusion, the present thesis provides techniques which enable an enhanced utilization of textual data, hence, supporting research in epigenomics and drug discovery