Dr. Ahmad Aghaebrahimian
Dr. Ahmad Aghaebrahimian
ZHAW
School of Life Sciences and Facility Management
FS Bioinformatics
Schloss 1
8820 Wädenswil
Personal profile
Position at the ZHAW
www.zhaw.ch/icls/bioinformatics/en/
Expertise and research interests
Deep Learning
Machine Learning
Natural Language Processing
Bio-text analytics
Semantic Web
Educational background
2021 – present Senior Postdoc, Biomedical Text analytics, ZHAW School of Life Sciences and Facility Management
2018 – 2021: Postdoc, Text Analytics, and Deep Learning, ZHAW School of Engineering
2017 – 2018: Research Stay, Text mining and Deep Learning, University of Innsbruck, Austria
2015 – 2019: Ph.D. Computer Science focusing on Mathematical Linguistics, Charles University, Czech Republic
2011 – 2013: M.A. Applied Linguistics, Allame Tabataba’i University, with honors (summa cum laude), Iran
2007 – 2011: B.Sc. Computer Engineering (Double major), Iran University of Science and Technology (IUST) with honors (summa cum laude), Iran
2006 –2010: B.A. English Translation Studies, Iran
Professional milestones
2021 – present: Senior researcher, Literature-Based Discovery, ZHAW School of Life Sciences and Facility Management
2018 – 2021: Deputy Leader and senior researcher, Innosuiss project, ZHAW School of Engineering
2017 – 2018: Researher, Transbank, University of Innsbruck, Austria
2015 – 2019: Ph.D., PI Hybrid Deep Question Answering, Charles University, Czech
Membership of networks
Swiss Institute of Bioinformatics
Projects
- AI for colorectal cancer: towards the improved CMS classification and interpretability / Team member / Project ongoing
- Inferring Ancestral Insertion and Deletion Events in Genomic Sequences / Team member / Project completed
- Computational Literature-based Discovery Methods / Team member / Project completed
- AuSuM – Automatic Supply Chain Monitoring / Deputy project leader / Project completed
Publications
-
Lardos, Andreas; Aghaebrahimian, Ahmad; Koroleva, Anna; Sidorova, Julia; Wolfram, Evelyn; Anisimova, Maria; Gil, Manuel,
2022.
Frontiers in Bioinformatics.
2(827207).
Available from: https://doi.org/10.3389/fbinf.2022.827207
-
Aghaebrahimian, Ahmad; Anisimova, Maria; Gil, Manuel,
2022.
Ontology-aware biomedical relation extraction [paper].
In:
Sojka, Petr; Horák, Aleš; Kopeček, Ivan; Pala, Karel, eds.,
Text, Speech, and Dialogue.
25th International Conference on Text, Speech and Dialogue (TSD), Brno, Czech Republic, 6-9 September 2022.
Cham:
Springer.
pp. 160-171.
Lecture Notes in Computer Science ; 13502.
Available from: https://doi.org/10.1007/978-3-031-16270-1_14
-
Tuggener, Don; Aghaebrahimian, Ahmad,
2021.
The Sentence End and Punctuation Prediction in NLG text (SEPP-NLG) shared task 2021 [paper].
In:
Proceedings of the Swiss Text Analytics Conference 2021.
Swiss Text Analytics Conference – SwissText 2021, Online, 14-16 June 2021.
CEUR Workshop Proceedings.
Available from: https://doi.org/10.21256/zhaw-23258
-
Aghaebrahimian, Ahmad; Cieliebak, Mark,
2020.
Named entity disambiguation at scale [paper].
In:
Schilling, Frank-Peter; Stadelmann, Thilo, eds.,
Artificial Neural Networks in Pattern Recognition.
9th IAPR TC 3 Workshop on Artificial Neural Networks for Pattern Recognition (ANNPR'20), Winterthur, Switzerland, 2-4 September 2020.
Cham:
Springer.
pp. 102-110.
Lecture Notes in Computer Science ; 12294.
Available from: https://doi.org/10.1007/978-3-030-58309-5_8
-
Aghaebrahimian, Ahmad; Cieliebak, Mark,
2019.
Hyperparameter tuning for deep learning in natural language processing [paper].
In:
4th Swiss Text Analytics Conference (SwissText 2019), Winterthur, June 18-19 2019.
Swisstext.
Available from: https://doi.org/10.21256/zhaw-18993
-
Aghaebrahimian, Ahmad; Cieliebak, Mark,
2019.
Towards integration of statistical hypothesis tests into deep neural networks [paper].
In:
Proceedings of the 57th Annual Meeting of the Association for Computational Linguistics.
57th Annual Meeting of the Association for Computational Linguistics, Florence, Italy, 28 July - 2 August 2019.
Association for Computational Linguistics.
pp. 5551-5557.
Available from: https://doi.org/10.18653/v1/P19-1557
Publications before appointment at the ZHAW
2020
Aghaebrahimian, A., Stauder, A and Ustaszewski, M(2019), Testing the validity of Wikipedia categories for subject matter labelling of open-domain corpus data, Journal of Information Science, Sage Publications
2019
Aghaebrahimian, A., Ustaszewski M. and Stauder, A(2019), Highly Parallel Texts Enriched with Highly Useful Metadata? A Wikipedia Case Study Combining Machine Learning and Social Technology, Journal of Digital Scholarship in the Humanities, Oxford University Press
Aghaebrahimian, A., Ustaszewski M. and Stauder, A (2019), The TransBank Aligner: Cross-Sentence Alignment with Deep Neural Networks, In Proceedings of the 22nd International Conference on Text, Speech, and Dialogue (TSD), Ljubljana, Slovenia
2018
Aghaebrahimian, A., (2018), Deep Hybrid Question Answering, Ph.D. dissertation, Charles University, Faculty of Physics and Mathematics, Prague, Czech Republic
Aghaebrahimian, A., (2018), Deep Neural Networks at the Service of Multilingual Parallel Sentence Extraction, In Proceedings of the 27th International Conference on Computational Linguistics (COLING 2018), Santa Fe, New-Mexico, USA
Aghaebrahimian, A., (2018), Linguistically-Based Deep Unstructured Question Answering, In Proceedings of the Conference on Computational Natural Language Learning (CoNLL 2018), Brussels, Belgium
2017
Aghaebrahimian, A., (2017), Hybrid Deep Open-Domain Question Answering, In Proceedings of the 8th Language and Technology Conference (LTC), Poznan, Poland
Aghaebrahimian, A., (2017), Constrained Deep Answer Sentence Selection. 20th International Conference on Text, Speech, and Dialogue (TSD), Prague, Czech Republic
Aghaebrahimian, A., (2017), Quora Question Answer Dataset, 20th International Conference on Text, Speech, and Dialogue(TSD), Prague, Czech Republic
2016
Aghaebrahimian, A. and Jurcicek, F., (2016), Open-domain Factoid Question Answering via Knowledge Graph Search, In Proceedings of the Workshop on Human-Computer Question Answering at North American chapter of Association of Computational Linguistics (NAACL), San Diego, CA, USA
Aghaebrahimian, A. and Jurcicek, F., (2016), Constraint-Based Open-Domain Question Answering Using Knowledge Graph Search, 19th International Conference on Text, Speech, and Dialogue (TSD), LNAI 9924
2015
Aghaebrahimian A. and Jurcicek, F., (2015), Machine Learning for Semantic Parsing in Review, In proceeding of 7th Language and Technology Conference (LTC), Poznan, Poland
Aghaebrahimian, A. and Jurcicek, F.(2015), Constraint-based Statistical Spoken Dialogue Systems. Young Round table of Researchers of Spoken Dialogue Systems (YRRSDS)
Aghaebrahimian, A. (2015) Constraint-based Semantic Parsing, In Proceedings of the Week of Doctoral Studies, Charles University, Faculty of Mathematics and Physics
2014
Aghaebrahimian, A., Rahimirad, M., Ahmadi, A. & Khalilpour Alamdari, j.(2014), Dynamic Assessment of Writing Skill in Advanced EFL Iranian Learners, Procedia- Social and Behavioral Sciences
2013
Seyed Erfani, S. and Aghaebrahimian, A.,(2013), Web 2.0 Incorporated Dynamic Assessment to Assess Writing Ability of Iranian EFL Learners, Global Journal of Human Social Science, Volume XIII Issue XIV(2013), ISSN,2249-460X
Aghaebrahimian. A, (2013), Use of Different Cohesive Devices as a Discursive Mechanism in Different Genres, A Corpus-based Study, The first international conference on language learning and teaching, an interdisciplinary approach, Ferdowsi University, Mashhad, Iran
2012
Aghaebrahimian. A, (2012), Corpus-based Analysis of Lexical Cohesive Devices in ESP (computer) Texts, Allame Tabataba’i University, Tehran, Iran
Aghaebrahimian. A, (2012), Age, social class and expression of condolence, Allame Tabataba’i University, Tehran, Iran
Aghaebrahimian. A, (2012), CALL and Teaching Writing, Allame Tabataba’i University, Tehran, Iran.
Other publications
Teaching activity:
2021
Biomedical Natural Language Processing module 1
Bioinformatics: Semantic web lecture in University of Zurich (https://compbiozurich.org/UZH-BIO390/course-days/2021-11-23-Ahmad-Aghaebrahimian/)
Digital Health: Biomedical Text analytics in ZHAW department of engineering
2020
CAS Machine Intelligence: Machine Learning, ZHAW department of engineering
MSc. Thesis supervisor
Lirui Zhang Biomedical Relation Extraction with syntactic trees powered by Deep Learning: Ongoing
Tobias Fierz Webpage classification based on Machine Learning, Defended with a Perfect score
Workshops:
2021
Sentence End and Punctuation Prediction in NLG Text (SEPP)- Co-organizer, ZHAW: department of engineering (https://sites.google.com/view/sentence-segmentation/)