Optimization and Applications of Large-Scale Biomedical Event Networks

The overwhelming amount and unprecedented speed of publication in the biomedical domain make it difficult for life science researchers to acquire and maintain a broad view of the field and gather all information that would be relevant for their research. As a response to this problem, the BioNLP (Biomedical Natural Language Processing) community of researches has emerged and strives to assist life science researchers by developing modern natural language processing (NLP), information extraction (IE) and information retrieval (IR) methods that can be applied at large-scale, to scan the whole publicly available biomedical literature and extract and aggregate the information found within, while automatically normalizing the variability of natural language statements. Among different tasks, biomedical event extraction has received much attention within BioNLP community recently. Biomedical event extraction constitutes the identification of biological processes and interactions described in biomedical literature, and their representation as a set of recursive event structures. The 2009–2013 series of BioNLP Shared Tasks on Event Extraction have given raise to a number of event extraction systems, several of which have been applied at a large scale (the full set of PubMed abstracts and PubMed Central Open Access full text articles), leading to creation of massive biomedical event databases, each of which containing millions of events. Sinece top-ranking event extraction systems are based on machine-learning approach and are trained on the narrow-domain, carefully selected Shared Task training data, their performance drops when being faced with the topically highly varied PubMed and PubMed Central documents. Specifically, false-positive predictions by these systems lead to generation of incorrect biomolecular events which are spotted by the end-users. This thesis proposes a novel post-processing approach, utilizing a combination of supervised and unsupervised learning techniques, that can automatically identify and filter out a considerable proportion of incorrect events from large-scale event databases, thus increasing the general credibility of those databases. The second part of this thesis is dedicated to a system we developed for hypothesis generation from large-scale event databases, which is able to discover novel biomolecular interactions among genes/gene-products. We cast the hypothesis generation problem as a supervised network topology prediction, i.e predicting new edges in the network, as well as types and directions for these edges, utilizing a set of features that can be extracted from large biomedical event networks. Routine machine learning evaluation results, as well as manual evaluation results suggest that the problem is indeed learnable. This work won the Best Paper Award in The 5th International Symposium on Languages in Biology and Medicine (LBM 2013).

Cultural and linguistic context and lexical inferencing in English language learning: A case study

In an increasingly multilingual world, English language has kept a marked predominance as a global language. In many countries, English is the primary choice for foreign language learning. There is a long history of research in English language learning. The same applies for research in reading. A main interest since the 1970s has been the reading strategy defined as inferencing or guessing the meaning of unknown words from context. Inferencing has ben widely researched, however, the results and conclusions seem to be mixed. While some agree that inferencing is a useful strategy, others doubt its usefulness. Nevertheless, most of the research seem to agree that the cultural background affects comprehension and inferencing. While most of these studies have been done with texts and contexts created by the researches, little has been done using natural prose. The present study will attempt to further clarify the process of inferencing and the effects of the text’s cultural context and the linguistic background of the reader using a text that has not been created by the researcher. The participants of the study are 40 international students from Turku, Finland. Their linguistic background was obtained through a questionnaire and proved to be diverse. Think aloud protocols were performed to investigate their inferencing process and find connections between their inferences, comments, the text, and their linguistic background. The results show that: some inferences were made based on the participants’ world knowledge, experience, other languages, and English language knowledge; other inferences and comments were made based on the text, its use of language and vocabulary, and few cues provided by the author. The results from the present study and previous research seem to show that: 1) linguistic background is a source of information for inferencing but is not a major source; 2) the cultural context of the text affected the inferences made by the participants according to their closeness or distance from it.