Tsendsuren Munkhdalai

I am a researcher at Microsoft Research Maluuba, Montreal. I spent two years at UMass Medical School as a postdoc sitting right next to the neurology department. I got my PhD from the Department of Computer Science at Chungbuk National University, South Korea under the excellent supervision of Prof. Keun Ho Ryu.

My current research focus is meta learning, memory and attention systems, rapid and temporal adaptations and feedbacks in artificial neural nets for language and text understanding.

I have several years of experience in programming with java (EE), including swing, JSF, EJB, and JPA. In addition, I have recently been playing with Scala, Python, R and Lua. I got the opportunity to try deep learning frameworks like Torch, Chainer, MXNET and Keras, data processing tools like Mahout, Scikit-learn, Weka and Opencv (Javacv), NoSQL database systems including Hbase, Redis, MongoDB and Cassandra, indexing technologies such as Apache Solr and Lucene, distributed computing and storage tools like Hadoop, Spark and Scalding (for Hadoop) and some other systems for document processing pipelines.

I would like to do a few sport activities frequently: bodybuilding, soccer, volleyball and swimming. I also like to have a beer while playing pool and discussing ideas and technology.

News

Open source software

  • DeepText: An end-to-end biomedical event extraction system based on deep learning and recursive projection model, written in Scala and Lua (using Torch).
  • BANNER-CHEMDNER: A multi-domain named entity recognition system that can be used to identify chemical and drug mention, biomedical mention or disease mention from text, written in Java.

Publications

Refereed journals

  • Tsendsuren Munkhdalai and Keun Ho Ryu. DeepText: End-to-end biomedical event extraction via deep learning and recursive projection model. Bioinformatics, 2015 (in progress) [code]
  • Tsendsuren Munkhdalai, Meijing Li, Khuyagbaatar Batsuren, Hyeon Ah Park, Nak Hyeon Choi and Keun Ho Ryu. Incorporating domain knowledge in chemical and biomedical named entity recognition with word representations. Journal of Cheminformatics, 2015 [link|code]
  • Tsendsuren Munkhdlai, Oyun-Erdene Namsrai and Keun Ho Ryu. Self-training significance space of support vectors for imbalanced biomedical event data. BMC Bioinformatics, 2015 (accepted for a special issue of BIOT 2014) [code]
  • Tsendsuren Munkhdalai, Meijing Li, Unil Yun, Oyun-Erdene Namsrai and Keun Ho Ryu. An active co-training algorithm for biomedical named-entity recognition. Journal of Information Processing Systems, 2012 [link|java code available]
  • Meijing Li, Tsendsuren Munkhdalai, Xiuming Yu and Keun Ho Ryu. A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction. Mathematical Problems in Engineering, 2015
  • Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M Lowe, Roger A Sayle, Riza Batista-Navarro, Rafal Rak, Torsten Huber, Tim Rocktäschel, Sérgio Matos, David Campos, Buzhou Tang, Hua Xu, Tsendsuren Munkhdalai, Keun Ryu, SV Ramanan, Senthil Nathan, Slavko Žitnik, Marko Bajec, Lutz Weber, Matthias Irmer, Saber A Akhondi, Jan A Kors, Shuo Xu, Xin An, Utpal Sikdar, Asif Ekbal, Masaharu Yoshioka, Thaer M Dieb, Miji Choi, Karin Verspoor, Madian Khabsa, C Giles, Hongfang Liu, Komandur Ravikumar, Andre Lamurias, Francisco M Couto, Hong-Jie Dai, Richard Tsai, Caglar Ata, Tolga Can, Anabel Usié, Rui Alves, Isabel Segura-Bedmar, Paloma Martínez, Julen Oyarzabal and Alfonso Valencia. The CHEMDNER corpus of chemicals and drugs and its annotation principles. Journal of Cheminformatics, 2015 [link]
  • Erdenetuya Namsrai, Tsendsuren Munkhdalai, Meijing Li, Jung-Hoon Shin, Oyun- Erdene Namsrai and Keun Ho Ryu. A Feature Selection-based Ensemble Method for Arrhythmia Classification. Journal of Information Processing Systems, 2013

Conference proceedings

  • Tsendsuren Munkhdalai, Meijing Li, Khuyagbaatar Batsuren and Keun Ho Ryu. Towards a unified named entity recognition system: disease mention identification. In Proceedings of the 6th International Conference on Bioinformatics Models, Methods and Algorithms, 2015 [code]
  • Tsendsuren Munkhdalai, Oyun-Erdene Namsrai and Keun Ho Ryu. Self-training significance space of support vectors for imbalanced biomedical event data. In Proceedings of the 11th Annual Biotechnology and Bioinformatics Symposium, 2014 [code]
  • Tsendsuren Munkhdalai, Meijing Li, Khuyagbaatar Batsuren and Wan-Sup Cho. Biomedical event extraction with random forests. In Proceedings of the 7th International Conference on the Frontiers of Information Technology, Application and Tools, 2014
  • Tsendsuren Munkhdalai, Meijing Li, Khuyagbaatar Batsuren and Keun Ho Ryu. BANNER-CHEMDNER: Incorporating domain knowledge in chemical and drug named entity recognition. In Proceedings of the 4th BioCreative Challenge Evaluation Workshop vol. 2, 2013 [code]
    Placed 6th (out of 23) in the CHEMDNER chemical document indexing subtask and 8th (out of 26) in the Chemical entity mention recognition subtask
  • Tsendsuren Munkhdalai, Meijing Li, Khuyagbaatar Batsuren and Keun Ho Ryu. A computational approach for biomedical event extraction. In Proceedings of the 6th International Conference on the Frontiers of Information Technology, Application and Tools, 2013
  • Tsendsuren Munkhdalai, Meijing Li, Taewook Kim, Oyun-Erdene Namsrai, Sunny Jeong, Jungpil Shin and Keun Ho Ryu. Biomedical named entity recognition based on co-training algorithm. In Proceedings of the 26th IEEE International Conference on Advanced Information Networking and Applications, 2012
  • Tsendsuren Munkhdalai, Meijing Li, Erdenetuya Namsrai, Oyun-Erdene Namsrai and Keun Ho Ryu. BFSM: Finite state machine learned as named boundary definer for bio named entity recognition. In Proceedings of the 3rd IEEE International Conference on Awareness Science and Technology, 2011.
  • Li Meijing,Tsendsuren Munkhdalai, Khuyagbaatar Batsuren and Keun Ho Ryu. A bio-document clustering system based on multiple similarity calculation method. In Proceedings of the 7th International Conference on the Frontiers of Information Technology, Application and Tools, 2014
  • Khuyagbaatar Batsuren, Tsendsuren Munkhdalai, Meijing Li and Keun Ho Ryu. Keyword extraction using anti-pattern. In Proceedings of the 7th International Conference on the Frontiers of Information Technology, Application and Tools, 2014
    The best paper award
  • Khuyagbaatar Batsuren, Tsendsuren Munkhdalai, Li Meijing, Namsrai Erdenetuya and Keun Ho Ryu. A novel method for SMS spam filtering using multiple features. In Proceedings of the 6th International Conference on the Frontiers of Information Technology, Application and Tools, 2013
  • Eonseok Shin, Munkhdalai Tsendsuren, Li Meijing, Incheon Paik and Keun Ho Ryu. Self-Training with active example selection criterion for biomedical named entity recognition. In Proceedings of 6th International Conference on Convergence and Hybrid Information Technology, 2012
  • Namsrai Erdenetuya, Munkhdalai Tsendsuren, Li Meijing and Keun Ho Ryu. An ensemble method for classification of arrhythmia with feature selection. In Proceedings of The 22nd International conference on Genome Informatics, 2011
  • Li Meijing, Munkhdalai Tsendsuren, Taewook Kim, Li Peipei and Keun Ho Ryu. A bio-text mining system for protein-protein interaction extraction. In Proceedings of The International Conference on Ubiquitous Healthcare, 2011

CV (available upon request)