Publications

[1] George Gkotsis, Anika Oellrich, Sumithra Velupillai, Maria Liakata, Tim J. P.
Hubbard, Richard J. B. Dobson, and Rina Dutta.
Characterisation of mental health conditions in social media using
informed deep learning.
Scientific Reports, 7:45141 EP –, 03 2017.
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[2] Sumithra Velupillai, Danielle Mowery, Mike Conway, John Hurdle, and Brent
Kious.
Vocabulary Development To Support Information Extraction of
Substance Abuse from Psychiatry Notest.
In Proceedings of BioNLP 2016, pages 92–101, Berlin, Germany,
August 2016. Association for Computational Linguistics.
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[3] Janani Kalyanam, Sumithra Velupillai, Mike Conway, and Gert Lanckriet.
From event detection to story telling on microblogs.
In ACM/IEEE Conference on Advances in Social Networks Analysis
and Mining (ASONAM 2016)
. 2016.
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[4] Danielle L Mowery, Brett R South, Lee Christensen, Jianwei Leng, Laura-Maria
Peltonen, Sanna Salanterä, Hanna Suominen, David Martinez, Sumithra
Velupillai, Noémie Elhadad, et al.
Normalizing acronyms and abbreviations to aid patient understanding
of clinical texts: ShARe/CLEF eHealth Challenge 2013, Task 2.
Journal of Biomedical Semantics, 7(1):1, 2016.
bib ]

[5] Abdulrahman AAl Abdulsalam, Sumithra Velupillai, and Stephane Meystre.
UtahBMI at SemEval-2016 Task 12: Extracting Temporal Information
from Clinical Text.
In Proceedings of the 10th International Workshop on Semantic
Evaluation (SemEval-2016)
, pages 1256–1262, San Diego, California, June
2016. Association for Computational Linguistics.
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[6] Gintarė Grigonytė, Maria Kvist, Mats Wirén, Sumithra Velupillai,
and Aron Henriksson.
Swedification patterns of Latin and Greek affixes in clinical text.
Nordic Journal of Linguistics, 39(01):5–37, 2016.
bib ]

[7] George Gkotsis, Sumithra Velupillai, Anika Oellrich, Harry Dean, Maria Liakata,
and Rina Dutta.
Don’t Let Notes Be Misunderstood: A Negation Detection Method for
Assessing Risk of Suicide in Mental Health Records.
In Proceedings of the Third Workshop on Computational
Lingusitics and Clinical Psychology
, pages 95–105, San Diego, CA, USA, June
2016. Association for Computational Linguistics.
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[8] George Gkotsis, Anika Oellrich, Tim Hubbard, Richard Dobson, Maria Liakata,
Sumithra Velupillai, and Rina Dutta.
The language of mental health problems in social media.
In Proceedings of the Third Workshop on Computational
Lingusitics and Clinical Psychology
, pages 63–73, San Diego, CA, USA, June
2016. Association for Computational Linguistics.
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[9] S. Velupillai, D. L. Mowery, S. Abdelrahman, L. Christensen, and W. W. Chapman.
Towards a Generalizable Time Expression Model for Temporal Reasoning
in Clinical Notes.
In AMIA 2015 Proceedings, pages 1252–1259, San Francisco, USA,
November 2015. American Medical Informatics Association.
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[10] S. Velupillai, D. Mowery, B. R. South, M. Kvist, and H. Dalianis.
Recent advances in clinical natural language processing in support of
semantic analysis.
IMIA Yearbook of Medical Informatics, 10:183–193, 2015.
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[11] J. Kalyanam, S. Velupillai, S. Doan, M. Conway, and G.R.G. Lanckriet.
Facts and Fabrications about Ebola: A Twitter Based Study.
In Proc. ACM KDD Workshop on Connected Health in Big Data Era,
Sydney, Australia, August 2015.
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[12] S. Velupillai, M. Duneld, A. Henriksson, M. Kvist, M. Skeppstedt, and
H. Dalianis.
Louhi 2014: Special issue on health text mining and information
analysis.
BMC Medical Informatics and Decision Making, 15(Suppl. 2),
2015.
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[13] Hercules Dalianis, Aron Henriksson, Maria Kvist, Sumithra Velupillai, and
Rebecka Weegar.
Health bank – a workbench for data science applications in
healthcare.
In Proceedings of the CAiSE-2015 Industry Track co-located with
the 27th Conference on Advanced Information Systems Engineering – CAiSE
2015
, pages 1–18, Stockholm, Sweden, June 2015. CEUR.
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[14] Sumithra Velupillai, Danielle L Mowery, Samir Abdelrahman, Lee Christensen, and
Wendy Chapman.
Blulab: Temporal information extraction for the 2015 clinical
tempeval challenge.
In Proceedings of the 9th International Workshop on Semantic
Evaluation – SemEval 2015
, pages 814–818, Denver, Colorado, June 2015.
Association for Computational Linguistics.
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[15] S. Velupillai, D.L. Mowery, L. Christensen, N. Elhadad, S. Pradhan, G. Savova,
and WW Chapman.
Disease/Disorder Semantic Template Filling – Information Extraction
Challenge in the ShARe/CLEF eHealth Evaluation Lab 2014.
In Proceedings of AMIA 2014, Washington, DC, November 2014.
American Medical Informatics Association.
bib ]

[16] K. Smith, B. Megyesi, S. Velupillai, and M. Kvist.
Professional language in Swedish clinical text: Linguistic
characterization and comparative studies.
Nordic Journal of Linguistics, 2:297–327, 2014.
bib ]

[17] E. Lövestam, S Velupillai, and M Kvist.
Abbreviations in Swedish Clinical Text – use by three professions.
Studies in Health Technology and Informatics, 205:720–724,
August 2014.
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[18] Maria Kvist and Sumithra Velupillai.
SCAN: A Swedish Clinical Abbreviation Normalizer.
In Evangelos Kanoulas, Mihai Lupu, Paul Clough, Mark Sanderson, Mark
Hall, Allan Hanbury, and Elaine Toms, editors, Information Access
Evaluation. Multilinguality, Multimodality, and Interaction
, volume 8685 of
Lecture Notes in Computer Science, pages 62–73. Springer International
Publishing, 2014.
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[19] Liadh Kelly, Lorraine Goeuriot, Hanna Suominen, Tobias Schreck, Gondy Leroy,
DanielleL. Mowery, Sumithra Velupillai, WendyW. Chapman, David Martinez,
Guido Zuccon, and João Palotti.
Overview of the share/clef ehealth evaluation lab 2014.
In Evangelos Kanoulas, Mihai Lupu, Paul Clough, Mark Sanderson, Mark
Hall, Allan Hanbury, and Elaine Toms, editors, Information Access
Evaluation. Multilinguality, Multimodality, and Interaction
, volume 8685 of
Lecture Notes in Computer Science, pages 172–191. Springer
International Publishing, 2014.
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Keywords: Information Retrieval; Information Extraction; Information Visualisation; Evaluation; Medical Informatics; Test-set Generation; Text Classification; Text Segmentation

[20] Danielle Mowery, Sumithra Velupillai, Brett R. South, Lee Christensen, David
Martinez, Liadh Kelly, Lorraine Goeuriot, Noemie Elhadad, Sameer Pradhan,
Guergana Savova, and Chapman Wendy W.
Task 2: ShARe/CLEF eHealth Evaluation Lab 2014.
In L. Cappellato, N. Ferro, M. Halvey, and W. Kraaij, editors,
CLEF2014 Working Notes
, volume 1180, pages 31–42. CEUR-WS, September
2014.
bib ]

[21] Sumithra Velupillai.
Temporal expressions in swedish medical text — a pilot study.
In Proceedings of BioNLP 2014, pages 88–92, Baltimore,
Maryland, June 2014. Association for Computational Linguistics.
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[22] Danielle Mowery, Mindy Ross, Sumithra Velupillai, Stephane Meystre, Janyce
Wiebe, and Wendy Chapman.
Generating patient problem lists from the share corpus using snomed
ct/snomed ct core problem list.
In Proceedings of BioNLP 2014, pages 54–58, Baltimore,
Maryland, June 2014. Association for Computational Linguistics.
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[23] Gintare Grigonyte, Maria Kvist, Sumithra Velupillai, and Mats Wirén.
Improving readability of swedish electronic health records through
lexical simplification: First results.
In Proceedings of the 3rd Workshop on Predicting and Improving
Text Readability for Target Reader Populations — PITR
, pages 74–83,
Gothenburg, Sweden, April 2014. Association for Computational Linguistics.
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[24] S. Velupillai, M Skeppstedt, M Kvist, D Mowery, B. E. Chapman, H. Dalianis, and
W. W. Chapman.
Cue-based assertion classification for Swedish clinical text —
Developing a lexicon for pyConTextSwe.
Artificial Intelligence in Medicine, 61:137–144, 2014.
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[25] Eric-Oluf Svee, Maria Kvist, and Sumithra Velupillai.
Capturing and Representing Values for Requirements of Personal
Health Records.
In J. Grabis, M. Kirikova, J. Zdravkovic, and J. Stirna, editors,
Short Paper Proceedings of the 6th IFIP WG 8.1 Working Conference on
the Practice of Enterprise Modeling (PoEM 2013)
, volume 1023, pages
166–175. CEUR-WS, November 2013.
bib ]

[26] H Suominen, S Salantera, S Velupillai, WW Chapman, G Savova, N Elhadad,
S Pradhan, BR South, DL Mowery, GJF Jones, J Leveling, L Kelly, L Goeuriot,
D Martinez, and G Zuccon.
Overview of the ShARe/CLEF eHealth Evaluation Lab 2013.
In Pamela Forner, Henning Muller, Roberto Paredes, Paolo Rosso, and
Benno Stein, editors, Information Access Evaluation. Multilinguality,
Multimodality, and Visualization. 4th International Conference of the CLEF
Initiative, CLEF 2013, Valencia, Spain, September 23-26, 2013. Proceedings
,
volume 8138 2013 of Lecture Notes in Computer Science, pages 212–231.
Springer, September 2013.
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[27] Maria Kvist and Sumithra Velupillai.
Professional Language in Swedish Radiology Reports —
Characterization for Patient-Adapted Text Simplification.
In Proceedings of the Scandinavian Conference on Health
Informatics 2013
, Copenhagen, Denmark, August 2013. Linköping
University Electronic Press, Linköpings universitet.
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[28] Sumithra Velupillai, Omran Ibrahim, and Maria Kvist.
Functions for Personal Health Records in Sweden — Patient
Perspectives.
In Proceedings of the Scandinavian Conference on Health
Informatics 2013
, Copenhagen, Denmark, August 2013. Linköping
University Electronic Press, Linköpings universitet.
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[29] WW Chapman, D Hillert, S Velupillai, M Kvist, M Skeppstedt, BE Chapman,
M Conway, M Tharp, DL Mowery, and L Deleger.
Extending the NegEx Lexicon for Multiple Languages.
Studies in Health Technology and Informatics, 192:677–681,
August 2013.
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[30] Hideyuki Tanushi, Hercules Dalianis, Martin Duneld, Maria Kvist, Maria
Skeppstedt, and Sumithra Velupillai.
Negation Scope Delimitation in Clinical Text Using Three Approaches:
NegEx, PyConTextNLP and SynNeg.
In Proceedings of the 19th Nordic Conference of Computational
Linguistics (NODALIDA 2013) NEALT Proceedings Series 16
, Oslo, Norway, May
2013.
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[31] Sumithra Velupillai, Maria Skeppstedt, Maria Kvist, Danielle Mowery, Brian E.
Chapman, Hercules Dalianis, and Wendy W. Chapman.
Porting a rule-based assertion classifier for clinical text from
english to swedish.
In Proceedings of the 4th International Louhi Workshop on
Health Document Text Mining and Information Analysis – Louhi 2013
, Sydney,
Australia, February 2013.
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[32] Niklas Isenius, Sumithra Velupillai, and Maria Kvist.
Initial results in the development of scan: a swedish clinical
abbreviation normalizer.
In Proceedings of the CLEF 2012 Workshop on Cross-Language
Evaluation of Methods, Applications, and Resources for eHealth Document
Analysis – CLEFeHealth2012
, Rome, Italy, September 2012. CLEF.
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[33] Danielle L. Mowery, Sumithra Velupillai, and Wendy W. Chapman.
Medical diagnosis lost in translation — analysis of uncertainty and
negation expressions in english and swedish clinical texts.
In BioNLP: Proceedings of the 2012 Workshop on Biomedical
Natural Language Processing
, pages 56–64, Montreal, Canada, June 2012.
Association for Computational Linguistics.
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[34] Sumithra Velupillai.
Shades of Certainty — Annotation and Classification of Swedish
Medical Records
.
Doctoral thesis, Department of Computer and Systems Sciences,
Stockholm University, Stockholm, Sweden, April 2012.
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[35] S. Velupillai and M. Kvist.
Fine-grained Certainty Level Annotations Used for Coarser-grained
E-health Scenarios — Certainty Classification of Diagnostic Statements in
Swedish Clinical Text.
In A. F. Gelbukh, editor, Computational Linguistics and
Intelligent Text Processing. 13th International Conference, CICLing 2012,
Part II
, volume 7182 of Lecture Notes in Computer Science, pages
450–461, New Delhi, India, March 2012. Springer.
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[36] Sumithra Velupillai.
Automatic Classification of Factuality Levels — A Case Study on
Swedish Diagnoses and the Impact of Local Context.
In Proc. The Fourth International Symposium on Languages in
Biology and Medicine — LBM 2011
, Singapore, December 2011.
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[37] S. Velupillai, H. Dalianis, and M. Kvist.
Factuality Levels of Diagnoses in Swedish Clinical Text.
In A. Moen, S. K. Andersen, J. Aarts, and P. Hurlen, editors,
Proc. XXIII International Conference of the European Federation for Medical
Informatics — User Centred Networked Health Care
, pages 559 — 563, Oslo,
August 2011. IOS Press.
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[38] M. Kvist, M. Skeppstedt, S. Velupillai, and H. Dalianis.
Modeling human comprehension of swedish medical records for
intelligent access and summarization systems, a physician’s perspective.
In Proc. 9th Scandinavian Conference on Health Informatics,
SHI
, Oslo, August 2011.
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[39] H. Allvin, E. Carlsson, H. Dalianis, R. Danielsson-Ojala, V. Daudaravicius,
M. Hassel, D. Kokkinakis, H. Lundgren-Laine, G.H. Nilsson, Ø. Nytrø,
S. Salanterä, M. Skeppstedt, H. Suominen, and S. Velupillai.
Characteristics of Finnish and Swedish intensive care nursing
narratives: a comparative analysis to support the development of clinical
language technologies.
Journal of Biomedical Semantics, 2(Suppl 3):S1,
doi:10.1186/2041-1480-2-S3-S1(12):19–26, July 2011.
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[40] M. Hassel, A. Henriksson, and S. Velupillai.
Something Old, Something New — Applying a Pre-trained Parsing Model
to Clinical Swedish.
In Proc. 18th Nordic Conf. on Comp. Ling. – NODALIDA ’11, May
11-13 2011.
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[41] Sumithra Velupillai.
Semantic annotations in clinical documentation: exploring potentials
for future information retrieval.
In Proceedings of the third workshop on Exploiting semantic
annotations in information retrieval
, ESAIR ’10, pages 9–10, New York, NY,
USA, October 2010. ACM.
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Keywords: clinical documentation, information retrieval, semantic annotations

[42] Oscar Täckström, Sumithra Velupillai, Martin Hassel, Gunnar Eriksson,
Hercules Dalianis, and Jussi Karlgren.
Uncertainty detection as approximate max-margin sequence labelling.
In Proceedings of the Fourteenth Conference on Computational
Natural Language Learning
, pages 84–91, Uppsala, Sweden, July 2010.
Association for Computational Linguistics.
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[43] Sumithra Velupillai.
Towards a better understanding of uncertainties and speculations in
swedish clinical text – analysis of an initial annotation trial.
In Proceedings of the Workshop on Negation and Speculation in
Natural Language Processing
, pages 14–22, Uppsala, Sweden, July 10 2010.
University of Antwerp.
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[44] Aron Henriksson and Sumithra Velupillai.
Levels of certainty in knowledge-intensive corpora: An initial
annotation study.
In Proceedings of the Workshop on Negation and Speculation in
Natural Language Processing
, pages 41–45, Uppsala, Sweden, July 10 2010.
University of Antwerp.
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[45] Helen Allvin, Elin Carlsson, Hercules Dalianis, Riitta Danielsson-Ojala, Vidas
Daudaravicius, Martin Hassel, Dimitrios Kokkinakis, Heljä Lundgren-Laine,
Gunnar Nilsson, Øystein Nytrø, Sanna Salanterä, Maria Skeppstedt,
Hanna Suominen, and Sumithra Velupillai.
Characteristics and analysis of finnish and swedish clinical
intensive care nursing narratives.
In Proceedings of the NAACL HLT 2010 Second Louhi Workshop on
Text and Data Mining of Health Documents
, pages 53–60, Los Angeles,
California, USA, June 2010. Association for Computational Linguistics.
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[46] Hercules Dalianis and Sumithra Velupillai.
De-identifying Swedish Clinical Text – Refinement of a Gold Standard
and Experiments with Conditional Random Fields.
Journal of Biomedical Semantics, 1(6), April 12 2010.
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[47] Hercules Dalianis and Sumithra Velupillai.
How Certain are Clinical Assessments? Annotating Swedish Clinical
Text for (Un)certainties, Speculations and Negations.
In Proceedings of the of the Seventh International Conference on
Language Resources and Evaluation, LREC 2010
, Valletta, Malta, May 19-21
2010.
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[48] Sumithra Velupillai, Martin Hassel, and Hercules Dalianis.
chapter Finding the Parallel: Automatic Dictionary Construction and
Identification of Parallel Text Pairs, pages 312–336.
Cambridge Scholars Publishing, February 2010.
ISBN(13): 978-1-4438-1755-4, ISBN(10): 1-4438-1755-4.
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[49] Hercules Dalianis and Sumithra Velupillai.
De-identifying Swedish Clinical Text – Refinement of a Gold Standard
and Experiments with Conditional Random Fields.
In Proceedings of The 3rd International Symposium on Languages
in Biology and Medicine – LBM ’09
, Seogwipo-si, Jeju Island, South Korea,
November 8-10 2009.
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[50] Hercules Dalianis, Gunnar H. Nilsson, and Sumithra Velupillai.
Is De-identification of Electronic Health Records Possible? OR Can
We Use Health Record Corpora for Research?
In Panel at Virtual Healthcare Interaction – VHI 09,
Association for the Advancement of Artificial Intelligence, Technical Report
FS-09-07
, AAAI 2009 Fall Symposium Series, pages 2–3, Arlington, VA, USA,
November 4-7 2009.
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[51] Hercules Dalianis, Martin Hassel, and Sumithra Velupillai.
The Stockholm EPR Corpus – Characteristics and Some Initial
Findings.
In Proceedings of ISHIMR 2009, Evaluation and implementation of
e-health and health information initiatives: international perspectives. 14th
International Symposium for Health Information Management Research
, Kalmar,
Sweden, October 14-16 2009.
Awarded best paper.
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[52] S. Velupillai, H. Dalianis, M. Hassel, and G. H. Nilsson.
Developing a standard for de-identifying electronic patient records
written in Swedish: Precision, recall and F-measure in a manual and
computerized annotation trial.
Int. J. Med. Inform. (2009),
doi:10.1016/j.ijmedinf.2009.04.005
, 78(12):19–26, 2009.
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[53] Yvonne Samuelsson, Oscar Täckström, and Sumithra Velupillai.
Evaluation of local features for argument identification and
classification for semantic role labeling.
In Proceedings of The Second Swedish Language Technology
Conference – SLTC-08
, page 2, Stockholm, Sweden, November 20-21 2008.
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[54] Sumithra Velupillai, Martin Hassel, and Hercules Dalianis.
Automatic Dictionary Construction and Identification of Parallel
Text Pairs.
In Proceedings of UCCTS`08 – The international symposium on
Using Corpora in Contrastive and Translation Studies
, Hangzhou, China,
September 25-27 2008.
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[55] Sumithra Velupillai, Hercules Dalianis, and Martin Hassel.
Diagnosing Diagnoses in Swedish Clinical Records.
In H. Karsten, B. Back, T. Salakoski, S. Salanterä, and
H. Suominen, editors, Proceedings of LOUHI `08 – The First Conference on
Text and Data Mining of Clinical Documents
, pages 110–112, Turku, Finland,
September 3-4 2008.
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[56] Sumithra Velupillai and Hercules Dalianis.
Automatic construction of domain-specific dictionaries on sparse
parallel corpora in the nordic languages.
In Coling 2008: Proceedings of the workshop Multi-source
Multilingual Information Extraction and Summarization
, pages 10–16,
Manchester, UK, August 23 2008. Coling 2008 Organizing Committee.
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[57] Yvonne Samuelsson, Oscar Täckström, Sumithra Velupillai, Johan Eklund,
Mark Fishel, and Markus Saers.
Mixing and blending syntactic and semantic dependencies.
In Proceedings of CoNLL 2008: Proceedings of the Twelfth
Conference on Computational Natural Language Learning
, Manchester, England,
August 16-17 2008.
Publisher: Coling 2008 Organizing Committee. Pages: 248 – 252.
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[58] M. Rosell and S. Velupillai.
Revealing relations between open and closed answers in questionnaires
through text clustering evaluation.
In European Language Resources Association (ELRA), editor, Proc.
of the 6th Int. Language Resources and Evaluation – LREC’08
, May 28-30 2008.
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[59] M. Rosell and S. Velupillai.
The Impact of Phrases in Document Clustering for Swedish.
In Proc. 15th Nordic Conf. on Comp. Ling. – NODALIDA ’05, May
20-21 2005.
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[60] Sumithra Velupillai.
Swedish Health Data – Information Access and Representation.
Licentiate thesis, Department of Computer and Systems Sciences,
Stockholm University, Stockholm, Sweden, October 2009.
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