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List of works by Sampo Pyysalo

A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text

scientific article (publication date: July 2013)

A neural classification method for supporting the creation of BioVerbNet

A neural network multi-task learning approach to biomedical named entity recognition

scientific article published on 15 August 2017

A re-evaluation of biomedical named entity-term relations ⬇️

scientific article published on 01 October 2010

All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning

scientific article

An analysis of gene/protein associations at PubMed scale

scientific article published on 6 October 2011

Analysis of Link Grammar on Biomedical Dependency Corpus Targeted at Protein-Protein Interactions ⬇️

scientific article published in 2004

Anatomical entity mention recognition at literature scale

scientific article

BLOOM: A 176B-Parameter Open-Access Multilingual Language Model ⬇️

scientific article published on 9 November 2022

Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine

scientific article

BioCause: Annotating and analysing causality in the biomedical domain

scientific article

BioInfer: a corpus for information extraction in the biomedical domain

scientific article

Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer

scientific article published on 14 July 2017

Cell line name recognition in support of the identification of synthetic lethality in cancer from text

scientific article published on October 2015

Combining hidden Markov models and latent semantic analysis for topic segmentation and labeling: method and clinical application

scientific article published on 26 March 2009

Comparative analysis of five protein-protein interaction corpora

scientific article

Complex event extraction at PubMed scale

scientific article

Dependency parsing of biomedical text with BERT

scientific article published on 29 December 2020

Entities, relations, events: representing biomolecular semantics.

scientific article published on 20 September 2010

Evaluation of two dependency parsers on biomedical corpus targeted at protein-protein interactions.

scientific article published on 11 August 2005

Event extraction across multiple levels of biological organization

scientific article

Event extraction for DNA methylation

scientific article published on 6 October 2011

Event extraction for systems biology by text mining the literature

scientific article

Event extraction on PubMed scale.

scientific article published on 6 October 2010

Generalising semantic category disambiguation with large lexical resources for fun and profit

scientific article

Improving the inter-corpora compatibility for protein annotations ⬇️

scientific article published on 01 October 2010

Intrinsic Evaluation of Word Vectors Fails to Predict Extrinsic Performance ⬇️

scientific article published in August 2016

Investigating heterogeneous protein annotations toward cross-corpora utilization

scientific article

LION LBD: a Literature-Based Discovery System for Cancer Biology

scientific article published on 01 May 2019

Large-scale event extraction from literature with multi-level gene normalization

scientific article

Lexical adaptation of link grammar to the biomedical sublanguage: a comparative evaluation of three approaches

scientific article

Medie and Info-pubmed: 2010 update.

scientific article published on 6 October 2010

Multi-CrossRE A Multi-Lingual Multi-Domain Dataset for Relation Extraction ⬇️

Named entity recognition for bacterial Type IV secretion systems

scientific article

Neural networks for link prediction in realistic biomedical graphs: a multi-dimensional evaluation of graph embedding-based approaches.

scientific article

Ontology design patterns to disambiguate relations between genes and gene products in GENIA

scientific article published on 6 October 2011

Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013.

scientific article published on 13 July 2015

Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011

scientific article

Sharing annotations better: RESTful Open Annotation ⬇️

scientific article (publication date: 2015)

Silver Syntax Pre-training for Cross-Domain Relation Extraction ⬇️

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets

scientific article published on 25 November 2020

Towards automated processing of clinical Finnish: sublanguage analysis and a rule-based parser.

scientific article published on 18 March 2009

U-Compare bio-event meta-service: compatible BioNLP event extraction services

scientific article (publication date: 18 December 2011)

Universal Dependencies v2: An Evergrowing Multilingual Treebank Collection ⬇️

Wide coverage biomedical event extraction using multiple partially overlapping corpora

scientific article

WikiBERT models: deep transfer learning for many languages ⬇️

scientific article

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