GERBIL: General Entity Annotator Benchmarking Framework

We present GERBIL, an evaluation framework for semantic entity annotation. The rationale behind our framework is to provide developers, end users and researchers with easy-to-use interfaces that allow for the agile, fine-grained and uniform evaluation of annotation tools on multiple datasets. By these means, we aim to ensure that both tool developers and end users can derive meaningful insights pertaining to the extension, integration and use of annotation applications. In particular, GERBIL provides comparable results to tool developers so as to allow them to easily discover the strengths and weaknesses of their implementations with respect to the state of the art. With the permanent experiment URIs provided by our framework, we ensure the reproducibility and archiving of evaluation results. Moreover, the framework generates data in machine-processable format, allowing for the efficient querying and post-processing of evaluation results. Finally, the tool diagnostics provided by GERBIL allows deriving insights pertaining to the areas in which tools should be further refined, thus allowing developers to create an informed agenda for extensions and end users to detect the right tools for their purposes. GERBIL aims to become a focal point for the state of the art, driving the research agenda of the community by presenting comparable objective evaluation results

Automatic extraction of robotic surgery actions from text and kinematic data

The latest generation of robotic systems is becoming increasingly autonomous due to technological advancements and artificial intelligence. The medical field, particularly surgery, is also interested in these technologies because automation would benefit surgeons and patients. While the research community is active in this direction, commercial surgical robots do not currently operate autonomously due to the risks involved in dealing with human patients: it is still considered safer to rely on human surgeons' intelligence for decision-making issues. This means that robots must possess human-like intelligence, including various reasoning capabilities and extensive knowledge, to become more autonomous and credible. As demonstrated by current research in the field, indeed, one of the most critical aspects in developing autonomous systems is the acquisition and management of knowledge. In particular, a surgical robot must base its actions on solid procedural surgical knowledge to operate autonomously, safely, and expertly. This thesis investigates different possibilities for automatically extracting and managing knowledge from text and kinematic data. In the first part, we investigated the possibility of extracting procedural surgical knowledge from real intervention descriptions available in textbooks and academic papers on the robotic-surgical domains, by exploiting Transformer-based pre-trained language models. In particular, we released SurgicBERTa, a RoBERTa-based pre-trained language model for surgical literature understanding. It has been used to detect procedural sentences in books and extract procedural elements from them. Then, with some use cases, we explored the possibilities of translating written instructions into logical rules usable for robotic planning. Since not all the knowledge required for automatizing a procedure is written in texts, we introduce the concept of surgical commonsense, showing how it relates to different autonomy levels. In the second part of the thesis, we analyzed surgical procedures from a lower granularity level, showing how each surgical gesture is associated with a given combination of kinematic data

LINKING ENTITIES TO A KNOWLEDGE BASE

Ph.DDOCTOR OF PHILOSOPH

B!SON: A Tool for Open Access Journal Recommendation

Finding a suitable open access journal to publish scientific work is a complex task: Researchers have to navigate a constantly growing number of journals, institutional agreements with publishers, funders’ conditions and the risk of Predatory Publishers. To help with these challenges, we introduce a web-based journal recommendation system called B!SON. It is developed based on a systematic requirements analysis, built on open data, gives publisher-independent recommendations and works across domains. It suggests open access journals based on title, abstract and references provided by the user. The recommendation quality has been evaluated using a large test set of 10,000 articles. Development by two German scientific libraries ensures the longevity of the project

Empirical studies on word representations

One of the most fundamental tasks in natural language processing is representing words with mathematical objects (such as vectors). The word representations, which are most often estimated from data, allow capturing the meaning of words. They enable comparing words according to their semantic similarity, and have been shown to work extremely well when included in complex real-world applications. A large part of our work deals with ways of estimating word representations directly from large quantities of text. Our methods exploit the idea that words which occur in similar contexts have a similar meaning. How we define the context is an important focus of our thesis. The context can consist of a number of words to the left and to the right of the word in question, but, as we show, obtaining context words via syntactic links (such as the link between the verb and its subject) often works better. We furthermore investigate word representations that accurately capture multiple meanings of a single word. We show that translation of a word in context contains information that can be used to disambiguate the meaning of that word

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