Kai Hakala


Doctoral Candidate, Language and Speech Technology (Department of Future Technologies)
Doctoral Student, Language and Speech Technology (Department of Future Technologies)

kahaka@utu.fi
+358 2 333 7649
Vesilinnantie 5
Turku




Publications

Data and systems for medication-related text classification and concept normalization from Twitter: insights from the Social Media Mining for Health (SMM4H)-2017 shared task (2018)
Journal of the American Medical Informatics Association
Abeed Sarker, Maksim Belousov, Jasper Friedrichs, Kai Hakala, Svetlana Kiritchenko, Farrokh Mehryary, Sifei Han, Tung Tran, Anthony Rios, Ramakanth Kavuluru, Berry de Bruijn, Filip Ginter, Debanjan Mahata, Saif M. Mohammad, Goran Nenadic, Graciela Gonzalez-Hernandez
(
A1 Journal article – refereed)

Evaluation of a Prototype System that Automatically Assigns Subject Headings to Nursing Narratives Using Recurrent Neural Network (2018) Proceedings of the 9th International Workshop on Health Text Mining and Information Analysis (LOUHI 2018) Hans Moen, Kai Hakala, Laura-Maria Peltonen, Henry Suhonen, Petri Loukasmäki, Tapio Salakoski, Filip Ginter, Sanna Salanterä
(
A4 Article in conference proceedings)

TurkuNLP Entry for Interactive Bio-ID Assignment (2018) Proceedings of the BioCreative VI Workshop Suwisa Kaewphan, Farrokh Mehryary, Kai Hakala, Tapio Salakoski, Filip Ginter
(
A4 Article in conference proceedings)

Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling (2018)
Database: The Journal of Biological Databases and Curation
Suwisa Kaewphan, Kai Hakala, Niko Miekka, Tapio Salakoski, Filip Ginter
(
A1 Journal article – refereed)

Detecting mentions of pain and acute confusion in Finnish clinical text (2017) SIGBioMed Workshop on Biomedical Natural Language: Proceedings of the 16th BioNLP Workshop Hans Moen, Kai Hakala, Farrokh Mehryary, Laura-Maria Peltonen, Tapio Salakoski, Filip Ginter, Sanna Salanterä
(
A4 Article in conference proceedings)

End-to-End System for Bacteria Habitat Extraction (2017) SIGBioMed Workshop on Biomedical Natural Language: Proceedings of the 16th BioNLP Workshop Farrokh Mehryary, Kai Hakala, Suwisa Kaewphan, Jari Björne, Tapio Salakoski, Filip Ginter
(
A4 Article in conference proceedings)

Ensemble of Convolutional Neural Networks for Medicine Intake Recognition in Twitter (2017)
CEUR Workshop Proceedings
Proceedings of the 2nd Social Media Mining for Health Research and Applications Workshop (SMM4H 2017) Kai Hakala, Farrokh Mehryary, Hans Moen, Suwisa Kaewphan, Tapio Salakoski, Filip Ginter
(
A4 Article in conference proceedings)

An expanded evaluation of protein function prediction methods shows an improvement in accuracy (2016)
GENOME BIOLOGY
Jiang YX, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo DCE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SME, Martelli PL, Profiti G, Casadio R, Cao RZ, Zhong Z, Cheng JL, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Toronen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Dukka BKC, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang HX, Paccanaro A, Gillis J, Sedeno-Cortes AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong QT, Ning W, Zhou YP, Tian WD, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SCE, del Pozo A, Fernandez JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk ADJ, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-e-Silva DC, Vencio RZN, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJE, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P
(
A1 Journal article – refereed)

Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification (2016)
Journal of Biomedical Semantics
Mehryary F, Kaewphan S, Hakala K, Ginter F
(
B1 Journal article)

Syntactic analyses and named entity recognition for PubMed and. PubMed Central — up-to-the-minute (2016) Proceedings of the 15th Workshop on Biomedical Natural Language Processing (BioNLP) Kai Hakala, Suwisa Kaewphan, Tapio Salakoski, Filip Ginter
(
A4 Article in conference proceedings)

Application of the EVEX resource to event extraction and network construction: Shared Task entry and result analysis (2015)
BMC Bioinformatics
Kai Hakala, Sofie Van Landeghem, Tapio Salakoski, Yves Van de Peer, Filip Ginter
(
A1 Journal article – refereed)

Sharing annotations better: RESTful Open Annotation (2015) Proceedings of ACL-IJCNLP 2015 System Demonstrations Pyysalo Sampo, Campos Jorge, Cejuela Juan Miguel, Ginter Filip, Hakala Kai, Li Chen, Stenetorp Pontus, Jensen Lars Juhl
(
A4 Article in conference proceedings)

UTU: Adapting Biomedical Event Extraction System to Disorder Attribute Detection (2015) The 9th International Workshop on Semantic Evaluation Kai Hakala
(
A4 Article in conference proceedings)

Eliminating Incorrect Events from Large‐Scale Event Networks by Trigger Word Clustering and Pruning (2014) Proceedings of the 6th International Symposium on Semantic Mining in Biomedicine (SMBM 2014) Farrokh Mehryary, Suwisa Kaewphan, Kai Hakala, Filip Ginter
(
A4 Article in conference proceedings)

UTU: Disease Mention Recognition and Normalization with CRFs and Vector Space Representations (2014) Proceedings of the 8th International Workshop on Semantic Evaluation (SemEval 2014) Suwisa Kaewphan, Kai Hakaka, Filip Ginter
(
A4 Article in conference proceedings)

EVEX in ST'13: Application of a large-scale text mining resource to event extraction and network construction (2013) Proceedings of the BioNLP Shared Task 2013 Workshop (BioNLP-ST'13) Kai Hakala, Sofie Van Landeghem, Tapio Salakoski, Yves Van de Peer, Filip Ginter
(
A4 Article in conference proceedings)

Hypothesis Generation in Large-Scale Event Networks (2013) Proceedings of the 5th International Symposium on Languages in Biology and Medicine (LBM'13) Hakala Kai, Mehryary Farrokh, Kaewphan Suwisa, Ginter Filip
(
A4 Article in conference proceedings)

Large-scale event extraction from literature with multi-level gene normalization (2013)
PLoS ONE
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
(
A1 Journal article – refereed)

CyEVEX: Literature-scale network integration and visualization through Cytoscape (2012) Hakala Kai, Van Landeghem Sofie, Kaewphan Suwisa, Salakoski Tapio, Van de Peer Yves, Ginter Filip
(
A4 Article in conference proceedings)

Exploring Biomolecular Literature with {EVEX}: Connecting Genes through Events, Homology and Indirect Associations (2012)
Advances in Bioinformatics
Van Landeghem S, Hakala K, Rönnqvist S, Salakoski T, Peer Y, Ginter F
(
A1 Journal article – refereed)


Last updated on 2019-24-07 at 02:22