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List of works by Tapio Salakoski

A large-scale evaluation of computational protein function prediction

scientific article

Accuracy of protein hydropathy predictions

article

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

scientific article

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

scientific article

An experimental comparison of cross-validation techniques for estimating the area under the ROC curve

article

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

scientific article published in 2004

Application of the EVEX resource to event extraction and network construction: Shared Task entry and result analysis

scientific article published on 30 October 2015

Applying language technology to nursing documents: pros and cons with a focus on ethics

scientific article published on 28 June 2007

Assessment of metal ion concentration in water with structured feature selection.

scientific article

Assisting nurses in care documentation: from automated sentence classification to coherent document structures with subject headings

scientific article published on 01 September 2020

Avoiding Hazards – What Can Health Care Learn from Aviation?

article

BioInfer: a corpus for information extraction in the biomedical domain

scientific article published on 9 February 2007

Building the essential resources for Finnish: the Turku Dependency Treebank

Can IT health-care applications improve the medication tray-filling process at hospital wards? An exploratory study using eye-tracking and stress response

article

Care episode retrieval: distributional semantic models for information retrieval in the clinical domain

scientific article

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

Comparison of automatic summarisation methods for clinical free text notes

scientific article published on 21 January 2016

Complex event extraction at PubMed scale

scientific article

Conditional Ranking on Relational Data

Contextual weighting for Support Vector Machines in literature mining: an application to gene versus protein name disambiguation

scientific article

Detecting biological associations between genes based on the theory of phase synchronization

scientific article published on 11 January 2008

Documentation of the Clinical Phase of the Cardiac Rehabilitation Process in a Finnish University Hospital District

Evaluating pain in intensive care

scientific article published in January 2009

Evaluation of Protein Hydropathy Scales

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

scientific article published on 11 August 2005

Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations

scientific article

Improving Layman Readability of Clinical Narratives with Unsupervised Synonym Replacement

Information flow in intensive care narratives

Interdisciplinary engineering education - Practice based case

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

scientific article

Learning Valued Relations from Data

Learning intransitive reciprocal relations with kernel methods

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

scientific article

Limits and Virtues of Educational Technology in Elementary School Mathematics

Mobile access to biological databases on the Internet

scientific article published on December 2002

Multiple different defense mechanisms are activated in the young transgenic tobacco plants which express the full length genome of the Tobacco mosaic virus, and are resistant against this virus.

scientific article published on 22 September 2014

Ontology Development for Patient Education Documents Using a Professional- and Patient-Oriented Delphi Method

article

Pain process of patients with cardiac surgery-Semantic annotation of electronic patient record data

scientific article published on 15 January 2019

Parallel Feature Selection for Regularized Least-Squares

article by Sebastian Okser et al published 2013 in Lecture Notes in Computer Science

Potent pairing: ensemble of long short-term memory networks and support vector machine for chemical-protein relation extraction

Predicting patient acuity from electronic patient records

scientific article published on 12 April 2014

Regularized Machine Learning in the Genetic Prediction of Complex Traits

scientific article (publication date: 13 November 2014)

Reverse engineering for gene regulatory networks by Bayesian orthogonal least squares (BOLS) algorithm

article

Secondary use of electronic health records: Availability aspects in two Nordic countries

scientific article published on 16 December 2018

Semantically linking molecular entities in literature through entity relationships

scientific article

Statistical parsing of varieties of clinical Finnish

scientific article published on 5 March 2014

Supporting the use of standardized nursing terminologies with automatic subject heading prediction: a comparison of sentence-level text classification methods

scientific article published on 01 January 2020

Syntactic analyses and named entity recognition for PubMed and PubMed Central — up-to-the-minute

TEES 2.2: Biomedical Event Extraction for Diverse Corpora

scientific article

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

scientific article published on 19 November 2019

Theoretical considerations of ethics in text mining of nursing documents

scientific article published on 01 January 2006

Tissue-specific expression of aryl hydrocarbon receptor and putative developmental regulatory modules in Baltic salmon yolk-sac fry.

scientific article published on 18 January 2008

Towards automated classification of intensive care nursing narratives

scientific article published on 01 January 2006

Towards automated classification of intensive care nursing narratives.

scientific article

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)

University of Turku in the BioNLP'11 Shared Task ⬇️

scientific article published on June 26, 2012

Unsupervised Phrase-Level Query Rewriting for Assisting Search in Clinical Free Text

scientific article published on 01 August 2019

Using cluster analysis to identify weak signals of lethal trends in aviation and healthcare documentation

article

Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling

Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations

scientific article

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