MASTERS THESIS DEFENSE: ZiLING FAN

Advisor: Nazli Goharian, Ph.D.

Title: Relation Extraction for Protein-protein Interactions Affected By Mutations

Date and Time: Thursday, APRIL 19 AT 4:00 PM

Location: ST. Mary’s Hall, 326 3700 Reservoir Road N.W., WASHINGTON

ABSTRACT: Precision Medicine (PM) is a promising approach for cancer treatment in the modern medical practice. Information about protein-protein interaction and mutations affecting the interaction is essential in understanding biological processes and is one of the key aims in PM research. While previous research in text mining has achieved great progress in extracting protein-protein interactions (PPIs) in biomedical literature, few efforts have been made to explore methods to extract PPIs which are affected by mutations. In this thesis, I propose a feature-rich supervised method to extract PPIs affected by mutations from biomedical literature. First, a supervised model is trained to predict if a pair of proteins is interacting for new instances. Next, a ‘mutation refinement’ step is incorporated as a filter to determine the final answer. I compared effectiveness of two different training corpora (i. BioCreative VI PM track training; ii. AIMed+BioInfer) for model training. Experimental result shows that supervised model trained with combined corpus (AIMed+BioInfer) achieved better performance. Additionally, features selected from previous PPI extraction work and additional features were tested for model training. Evaluation of the result using BioCreative VI PM track testing dataset proves the effectiveness of the features proposed in my method. The system achieves up to 44% to improvement in F1-score over baseline method.

 

DOCTORAL Dissertation Defense: Jiyun Luo

Advisor: Grace Hui Yang, Ph.D.

Title: Dynamic Search Models and Applicatins

Date and Time: Tuesday, April 17 AT 11:00 AM

Location: Regents Hall, 551 3700 O St, N.W., WASHINGTON

 

The 12th Semi-Annual GU-CS Graduate Research Presentation Day

Arman Cohan, Franck Dernoncourt, Doo Soon Kim, Trung Bui, Seokhwan Kim, Walter Chang, and Nazli Goharian , “A Discourse-Aware Attention Model for Abstractive Summarization of Long Documents”,  NAACL 2018 (to appear). – (short paper: 7 pages).

Sean MacAvaney, Luca Soldaini, Arman Cohan and Nazli Goharian, “Tree-LSTMs for Scientific Relation Classification”, SemEval 2018. -- (workshop; short: 4 pages)

Rob Churchill, Lisa Singh, Christo Kirov. "A Temporal Topic Model for Noisy Mediums”, The Pacific-Asia Conference on Knowledge Discovery and Data Mining. June 3-6, 2018.  -- (long)

Luca Soldaini, Timothy Walsh, Arman Cohan, Meng Han, Nazli Goharian, “Helping or Hurting? Predicting Changes in Users' Risk of Self-Harm through Online Community Interactions”, The Fifth Annual Computational Linguistics and Clinical Psychology Workshop (CLPsych’18), collocated with NAACL 2018.   (workshop: long – 10 pages).Presenter: Time  (20 min)

Sean MacAvaney and Amir Zeldes. "A Deeper Look into Dependency-Based Word Embeddings", NAACL Student Research Workshop 2018 -- (workshop, short)

Location: St. Mary's 326

Date and Time: Friday, April 27 at 1:00pm to 3:00pm

 

DOCTORAL Dissertation Defense: Luca Soldaini

 

Advisor: Nazli Goharian, Ph.D.

Title: The Knowledge and Language Gap in Medical Information Seeking

Date and Time: Monday, March 26 at 10:00am to 12:00pm

Location: St. Mary's 326

 

DOCTORAL Dissertation Defense: Brendan Sheridan

Advisor: Jeremy Fineman, Ph.D.

Title: Title: Parallel Scheduling with Batching

Date and Time: Friday, November 17, 2017 at 1:00pm to 3:00pm

Location: St. Mary's 124

DOCTORAL Dissertation Defense: Arman Cohan

Advisor:  Nazli Goharian, Ph.D.

Title: Text summarization and categorization for scientific and health-related data

Date and Time: Monday, March 19 at 10:00am to 12:00pm

Location: St. Mary's 326

 

DOCTORAL Dissertation Defense: Sicong Zhang

Advisor: Grace Hui Yang, Ph.D.

Title: Query Log Anonymization by Differential Privacy

Date and Time: Wednesday, October 25, 2017 at 3:00pm to 5:00pm

Location: STM 326

 

The 11th Semi-Annual GU-CS Graduate Research Presentation Day (Session II)

Session II   (10-12:15)

25 min: Yuankai Zhang, Adam O’Neill, Micah Sherr, and Wenchao Zhou. Privacy-preserving Network Provenance. Proceedings of the VLDB Endowment (PVLDB), August 2017. To appear. 

 

25 min: Sicong Zhang and Grace Hui Yang. Deriving Differentially Private Session Logs for Query Suggestion. In the 3rd ACM International Conference on the Theory of Information Retrieval (ICTIR 2017). October 2017. (To appear)

 

25 min: Arman Cohan, and Allan Fong, Raj Ratwani, and Nazli Goharian. "Identifying Harm Events in Clinical Care through Medical Narratives ", ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), August  2017.

 https://arxiv.org/pdf/1708.04681.pdf

 

25 min: Tavish Vaidya, Eric Burger, Micah Sherr, and Clay Shields. Where art thou, Eve? Experiences Laying Traps for Internet Eavesdroppers. In USENIX Workshop on Cyber Security Experimentation and Test (CSET), August 2017.  https://www.usenix.org/system/files/conference/cset17/cset17-paper-vaidya.pdf

Date and Time:  Friday Sep 22, 2017, 10AM

Location: St. Mary's 326

The 11th Semi-Annual GU-CS Graduate Research Presentation Day (Session II)

25 min: Andrew Yates*, Arman Cohan*, and Nazli Goharian. "Depression and Self-Harm Risk Assessment in Online Forums", Empirical Methods for Natural Language Processing (EMNLP), Sept 2017,   EMNLP’17 Best Long Paper Award   (  *Equal contribution )

15 min: Luca Soldaini, Andrew Yates, and Nazli Goharian. "Denoising Clinical Notes for Medical Literature Retrieval with Convolutional Neural Model." CIKM 2017. [to appear], Nov 2017.

25 min: Daniel Anderson, Pryce Bevan, Kevin Lang, Edo Liberty, Lee Rhodes, Justin Thaler. "A High-Performance Algorithm for Identifying Frequent Items in Data Streams" Internet Measurement Conference, November 2017.   https://arxiv.org/abs/1705.07001 

35 min: Arman Cohan and Nazli Goharian. "Scientific Document Summarization via Citation Contextualization and Scientific Discourse", International Journal on Digital Libraries (IJDL). Special Issue on Bibliometric-Enhanced Information Retrieval and Natural Language Processing 

https://arxiv.org/pdf/1706.03449.pdf 

15 min: Henri Maxime Demoulin*, Tavish Vaidya*, Isaac Pedisich, Nik Sultana, Yuankai Zhang, Ang Chen, Andreas Haeberlen, Boon Thau Loo, Linh Thi Xuan Phan, Micah Sherr, Clay Shields, and Wenchao Zhou.  A Demonstration of the DeDoS Platform for Defusing Asymmetric DDoS Attacks in Data Centers (Demo).  In Proceedings of SIGCOMM Posters and Demos ’17, Los Angeles, CA, USA, August 22–24, 2017, 3 pages. (* co-first authors).

Date and Time:  Thursday Oct 5, 2017, 11AM

Location: STM 326

 

The 11th Semi-Annual GU-CS Graduate Research Presentation Day (Session I)

 

 Session I : Sept 15th   (11:00-1:15)    

 

30 min: Arman Cohan, Sydney Young, Andrew Yates, Nazli Goharian. "Triaging Content Severity in Online Mental-Health Forums" Journal of the Association for Information Science and Technology (JASIST) [in press].

 http://ir.cs.georgetown.edu/downloads/jasist17-126.pdf

 

30 min: Luca Soldaini, Andrew Yates, and Nazli Goharian. "Learning to Reformulate Long Queries for Clinical Decision Support." Journal of the Association for Information Science and Technology (JASIST), Special Issue on Biomedical Information Retrieval. 

http://ir.cs.georgetown.edu/downloads/soldaini-jasist-cds.pdf

 

25 min: Zhiwen Tang, Grace Hui Yang, Investigating per Topic Upper Bound for Session Search Evaluation, The 3rd ACM International Conference on the Theory of Information Retrieval (ICTIR), October 2017 (to appear).

 

15 min: Sean MacAvaney, Kai Hui, Andrew Yates, An Approach for Weakly-Supervised Deep Information Retrieval,  Workshop on Neural Information Retrieval (Neu-IR '17), SIGIR 2017, August 2017

https://arxiv.org/abs/1707.00189

Date and Time:  Friday Sep 15, 2017, 11AM

Location: St. Mary's 326