Search Results - "Pyysalo, Sampo"

A neural network multi-task learning approach to biomedical named entity recognition by Crichton, Gamal, Pyysalo, Sampo, Chiu, Billy, Korhonen, Anna

“…Named Entity Recognition (NER) is a key task in biomedical text mining. Accurate NER systems require task-specific, manually-annotated datasets, which are…”
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The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets by Szklarczyk, Damian, Gable, Annika L, Nastou, Katerina C, Lyon, David, Kirsch, Rebecca, Pyysalo, Sampo, Doncheva, Nadezhda T, Legeay, Marc, Fang, Tao, Bork, Peer, Jensen, Lars J, von Mering, Christian

“…Abstract Cellular life depends on a complex web of functional associations between biomolecules. Among these associations, protein–protein interactions are…”
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Neural networks for link prediction in realistic biomedical graphs: a multi-dimensional evaluation of graph embedding-based approaches by Crichton, Gamal, Guo, Yufan, Pyysalo, Sampo, Korhonen, Anna

“…Link prediction in biomedical graphs has several important applications including predicting Drug-Target Interactions (DTI), Protein-Protein Interaction (PPI)…”
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Dependency parsing of biomedical text with BERT by Kanerva, Jenna, Ginter, Filip, Pyysalo, Sampo

“… : Syntactic analysis, or parsing, is a key task in natural language processing and a required component for many text mining approaches. In recent years,…”
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BioInfer: a corpus for information extraction in the biomedical domain by Pyysalo, Sampo, Ginter, Filip, Heimonen, Juho, Björne, Jari, Boberg, Jorma, Järvinen, Jouni, Salakoski, Tapio

“…Lately, there has been a great interest in the application of information extraction methods to the biomedical domain, in particular, to the extraction of…”
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Comparative analysis of five protein-protein interaction corpora by Pyysalo, Sampo, Airola, Antti, Heimonen, Juho, Björne, Jari, Ginter, Filip, Salakoski, Tapio

“…Growing interest in the application of natural language processing methods to biomedical text has led to an increasing number of corpora and methods targeting…”
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Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine by Chiu, Billy, Pyysalo, Sampo, Vulić, Ivan, Korhonen, Anna

“…Word representations support a variety of Natural Language Processing (NLP) tasks. The quality of these representations is typically assessed by comparing the…”
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Event extraction across multiple levels of biological organization by Pyysalo, Sampo, Ohta, Tomoko, Miwa, Makoto, Cho, Han-Cheol, Tsujii, Jun'ichi, Ananiadou, Sophia

“…Event extraction using expressive structured representations has been a significant focus of recent efforts in biomedical information extraction. However,…”
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Complex event extraction at PubMed scale by Björne, Jari, Ginter, Filip, Pyysalo, Sampo, Tsujii, Jun'ichi, Salakoski, Tapio

“…Motivation: There has recently been a notable shift in biomedical information extraction (IE) from relation models toward the more expressive event model,…”
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Large-scale event extraction from literature with multi-level gene normalization by Van Landeghem, Sofie, Björne, Jari, Wei, Chih-Hsuan, Hakala, Kai, Pyysalo, Sampo, Ananiadou, Sophia, Kao, Hung-Yu, Lu, Zhiyong, Salakoski, Tapio, Van de Peer, Yves, Ginter, Filip

“…Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of…”
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Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011 by Pyysalo, Sampo, Ohta, Tomoko, Rak, Rafal, Sullivan, Dan, Mao, Chunhong, Wang, Chunxia, Sobral, Bruno, Tsujii, Jun'ichi, Ananiadou, Sophia

“…We present the preparation, resources, results and analysis of three tasks of the BioNLP Shared Task 2011: the main tasks on Infectious Diseases (ID) and…”
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Correction to ‘The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets’ by Szklarczyk, Damian, Gable, Annika L, Nastou, Katerina C, Lyon, David, Kirsch, Rebecca, Pyysalo, Sampo, Doncheva, Nadezhda T, Legeay, Marc, Fang, Tao, Bork, Peer, Jensen, Lars J, von Mering, Christian

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A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text by Miwa, Makoto, Ohta, Tomoko, Rak, Rafal, Rowley, Andrew, Kell, Douglas B, Pyysalo, Sampo, Ananiadou, Sophia

“…To create, verify and maintain pathway models, curators must discover and assess knowledge distributed over the vast body of biological literature. Methods…”
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A neural classification method for supporting the creation of BioVerbNet by Chiu, Billy, Majewska, Olga, Pyysalo, Sampo, Wey, Laura, Stenius, Ulla, Korhonen, Anna, Palmer, Martha

“…VerbNet, an extensive computational verb lexicon for English, has proved useful for supporting a wide range of Natural Language Processing tasks requiring…”
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Event extraction on PubMed scale by Ginter, Filip, Björne, Jari, Pyysalo, Sampo

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Named entity recognition for bacterial Type IV secretion systems by Ananiadou, Sophia, Sullivan, Dan, Black, William, Levow, Gina-Anne, Gillespie, Joseph J, Mao, Chunhong, Pyysalo, Sampo, Kolluru, Balakrishna, Tsujii, Junichi, Sobral, Bruno

“…Research on specialized biological systems is often hampered by a lack of consistent terminology, especially across species. In bacterial Type IV secretion…”
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Event extraction for DNA methylation by Ohta, Tomoko, Pyysalo, Sampo, Miwa, Makoto, Tsujii, Jun'ichi

“…We consider the task of automatically extracting DNA methylation events from the biomedical domain literature. DNA methylation is a key mechanism of epigenetic…”
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Anatomical entity mention recognition at literature scale by Pyysalo, Sampo, Ananiadou, Sophia

“…Anatomical entities ranging from subcellular structures to organ systems are central to biomedical science, and mentions of these entities are essential to…”
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An analysis of gene/protein associations at PubMed scale by Pyysalo, Sampo, Ohta, Tomoko, Tsujii, Jun'ichi

“…Event extraction following the GENIA Event corpus and BioNLP shared task models has been a considerable focus of recent work in biomedical information…”
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U-Compare bio-event meta-service: compatible BioNLP event extraction services by Kano, Yoshinobu, Björne, Jari, Ginter, Filip, Salakoski, Tapio, Buyko, Ekaterina, Hahn, Udo, Cohen, K Bretonnel, Verspoor, Karin, Roeder, Christophe, Hunter, Lawrence E, Kilicoglu, Halil, Bergler, Sabine, Van Landeghem, Sofie, Van Parys, Thomas, Van de Peer, Yves, Miwa, Makoto, Ananiadou, Sophia, Neves, Mariana, Pascual-Montano, Alberto, Özgür, Arzucan, Radev, Dragomir R, Riedel, Sebastian, Sætre, Rune, Chun, Hong-Woo, Kim, Jin-Dong, Pyysalo, Sampo, Ohta, Tomoko, Tsujii, Jun'ichi

“…Bio-molecular event extraction from literature is recognized as an important task of bio text mining and, as such, many relevant systems have been developed…”
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