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Items: 1 to 20 of 37

1.

Comparison of automatic summarisation methods for clinical free text notes.

Moen H, Peltonen LM, Heimonen J, Airola A, Pahikkala T, Salakoski T, Salanterä S.

Artif Intell Med. 2016 Feb;67:25-37. doi: 10.1016/j.artmed.2016.01.003. Epub 2016 Jan 21.

2.

TEES 2.2: Biomedical Event Extraction for Diverse Corpora.

Björne J, Salakoski T.

BMC Bioinformatics. 2015;16 Suppl 16:S4. doi: 10.1186/1471-2105-16-S16-S4. Epub 2015 Oct 30.

3.

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

Hakala K, Van Landeghem S, Salakoski T, Van de Peer Y, Ginter F.

BMC Bioinformatics. 2015;16 Suppl 16:S3. doi: 10.1186/1471-2105-16-S16-S3. Epub 2015 Oct 30.

4.

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

Moen H, Ginter F, Marsi E, Peltonen LM, Salakoski T, Salanterä S.

BMC Med Inform Decis Mak. 2015;15 Suppl 2:S2. doi: 10.1186/1472-6947-15-S2-S2. Epub 2015 Jun 15.

5.

Regularized machine learning in the genetic prediction of complex traits.

Okser S, Pahikkala T, Airola A, Salakoski T, Ripatti S, Aittokallio T.

PLoS Genet. 2014 Nov 13;10(11):e1004754. doi: 10.1371/journal.pgen.1004754. eCollection 2014 Nov. No abstract available.

6.

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.

Jada B, Soitamo AJ, Siddiqui SA, Murukesan G, Aro EM, Salakoski T, Lehto K.

PLoS One. 2014 Sep 22;9(9):e107778. doi: 10.1371/journal.pone.0107778. eCollection 2014.

7.

Predicting patient acuity from electronic patient records.

Kontio E, Airola A, Pahikkala T, Lundgren-Laine H, Junttila K, Korvenranta H, Salakoski T, Salanterä S.

J Biomed Inform. 2014 Oct;51:35-40. doi: 10.1016/j.jbi.2014.04.001. Epub 2014 Apr 12.

8.

Statistical parsing of varieties of clinical Finnish.

Laippala V, Viljanen T, Airola A, Kanerva J, Salanterä S, Salakoski T, Ginter F.

Artif Intell Med. 2014 Jul;61(3):131-6. doi: 10.1016/j.artmed.2014.02.002. Epub 2014 Mar 5.

PMID:
24680097
9.

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

Van Landeghem S, Björne J, Wei CH, Hakala K, Pyysalo S, Ananiadou S, Kao HY, Lu Z, Salakoski T, Van de Peer Y, Ginter F.

PLoS One. 2013 Apr 17;8(4):e55814. doi: 10.1371/journal.pone.0055814. Print 2013.

10.

A large-scale evaluation of computational protein function prediction.

Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I.

Nat Methods. 2013 Mar;10(3):221-7. doi: 10.1038/nmeth.2340. Epub 2013 Jan 27.

11.

Semantically linking molecular entities in literature through entity relationships.

Van Landeghem S, Björne J, Abeel T, De Baets B, Salakoski T, Van de Peer Y.

BMC Bioinformatics. 2012 Jun 26;13 Suppl 11:S6. doi: 10.1186/1471-2105-13-S11-S6.

12.

University of Turku in the BioNLP'11 Shared Task.

Björne J, Ginter F, Salakoski T.

BMC Bioinformatics. 2012 Jun 26;13 Suppl 11:S4. doi: 10.1186/1471-2105-13-S11-S4.

13.

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

Van Landeghem S, Hakala K, Rönnqvist S, Salakoski T, Van de Peer Y, Ginter F.

Adv Bioinformatics. 2012;2012:582765. doi: 10.1155/2012/582765. Epub 2012 Jun 6.

14.

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

Pahikkala T, Okser S, Airola A, Salakoski T, Aittokallio T.

Algorithms Mol Biol. 2012 May 2;7(1):11. doi: 10.1186/1748-7188-7-11.

15.

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

Kano Y, Björne J, Ginter F, Salakoski T, Buyko E, Hahn U, Cohen KB, Verspoor K, Roeder C, Hunter LE, Kilicoglu H, Bergler S, Van Landeghem S, Van Parys T, Van de Peer Y, Miwa M, Ananiadou S, Neves M, Pascual-Montano A, Özgür A, Radev DR, Riedel S, Sætre R, Chun HW, Kim JD, Pyysalo S, Ohta T, Tsujii J.

BMC Bioinformatics. 2011 Dec 18;12:481. doi: 10.1186/1471-2105-12-481.

16.

Complex event extraction at PubMed scale.

Björne J, Ginter F, Pyysalo S, Tsujii J, Salakoski T.

Bioinformatics. 2010 Jun 15;26(12):i382-90. doi: 10.1093/bioinformatics/btq180.

17.

Accuracy of protein hydropathy predictions.

Jääskeläinen S, Riikonen P, Salakoski T, Vihinen M.

Int J Data Min Bioinform. 2010;4(6):735-54.

PMID:
21355504
18.

Evaluating pain in intensive care.

Suominen H, Lundgrén-Laine H, Salanterä S, Salakoski T.

Stud Health Technol Inform. 2009;146:192-6.

PMID:
19592833
19.

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

Ginter F, Suominen H, Pyysalo S, Salakoski T.

Int J Med Inform. 2009 Dec;78(12):e1-6. doi: 10.1016/j.ijmedinf.2009.02.003. Epub 2009 Mar 26.

PMID:
19328036
20.

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

Laippala V, Ginter F, Pyysalo S, Salakoski T.

Int J Med Inform. 2009 Dec;78(12):e7-12. doi: 10.1016/j.ijmedinf.2009.02.005. Epub 2009 Mar 18.

PMID:
19299195
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