Tapio Salakoski

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We describe a system for extracting complex events among genes and proteins from biomedical literature, developed in context of the BioNLP’09 Shared Task on Event Extraction. For each event, its text trigger, class, and arguments are extracted. In contrast to the prevailing approaches in the domain, events can be arguments of other events, resulting in a(More)
Lately, there has been a great interest in the application of information extraction methods to the biomedical domain, in particular, to the extraction of relationships of genes, proteins, and RNA from scientific publications. The development and evaluation of such methods requires annotated domain corpora. We present BioInfer (Bio Information Extraction(More)
Automated extraction of protein-protein interactions (PPI) is an important and widely studied task in biomedical text mining. We propose a graph kernel based approach for this task. In contrast to earlier approaches to PPI extraction, the introduced all-paths graph kernel has the capability to make use of full, general dependency graphs representing the(More)
In this paper, we propose a graph kernel based approach for the automated extraction of protein-protein interactions (PPI) from scientific literature. In contrast to earlier approaches to PPI extraction, the introduced alldependency-paths kernel has the capability to consider full, general dependency graphs. We evaluate the proposed method across five(More)
We present a system for extracting biomedical events (detailed descriptions of biomolecular interactions) from research articles. This system was developed for the BioNLP’11 Shared Task and extends our BioNLP’09 Shared Task winning Turku Event Extraction System. It uses support vector machines to first detect event-defining words, followed by detection of(More)
Growing interest in the application of natural language processing methods to biomedical text has led to an increasing number of corpora and methods targeting protein-protein interaction (PPI) extraction. However, there is no general consensus regarding PPI annotation and consequently resources are largely incompatible and methods are difficult to evaluate.(More)
We participate in the BioNLP 2013 Shared Task with Turku Event Extraction System (TEES) version 2.1. TEES is a support vector machine (SVM) based text mining system for the extraction of events and relations from natural language texts. In version 2.1 we introduce an automated annotation scheme learning system, which derives task-specific event rules and(More)
During the past few years, several novel text mining algorithms have been developed in the context of the BioNLP Shared Tasks on Event Extraction. These algorithms typically aim at extracting biomolecular interactions from text by inspecting only the context of one sentence. However, when humans interpret biomolecular research articles, they usually build(More)
Learning preference relations between objects of interest is one of the key problems in machine learning. Our approach for addressing this task is based on pairwise comparisons for estimation of overall ranking. In this paper, we propose a simple preference learning algorithm based on regularized least squares and describe it within the kernel methods(More)
Several incompatible syntactic annotation schemes are currently used by parsers and corpora in biomedical information extraction. The recently introduced Stanford dependency scheme has been suggested to be a suitable unifying syntax formalism. In this paper, we present a step towards such unification by creating a conversion from the Link Grammar to the(More)