about

Leila Safari

Biography

Dr. Leila Safari is an Assistant Professor at the Department of Computer & Electronic Engineering at the University of Zanjan in Iran. She received her PhD under supervision of Professor Jon Patrick, in Software Engineering from the University of Sydney, Australia, where her thesis focused on developing a Clinical Data Analytics Language (CliniDAL).

During her PhD studies she gained extensive experience in Clinical Data Analytics, Text Mining and utilizing NLP techniques to extract valuable insights from free text and structured data in the form of EAV (Entity Attribute Value), which is a common structure in most Clinical Information Systems (CISs).

To provide the required knowledge through data analytics, an appropriate tool is necessary. Due to the complexity of information extraction from clinical information systems (CISs) and the lack of integrated data analytics tools in most CISs, I have developed CliniDAL as a special purpose query language for Clinical Data Analytics (CliniDAL). In principle, CliniDAL users can compose a query in the restricted natural language interface, and it can compute answers to any question that is answerable from a CIS. Question and answer categories include:

  1. Point-of-care retrieval queries
  2. Descriptive statistics
  3. Statistical hypothesis testing
  4. Scientific experiment complex hypothesis testing
  5. Semantic record retrieval
  6. Predictive modeling

Here is the sample  grammar (formal definition) of the language which is published in her paper "Knowledge discovery and knowledge reuse in clinical information systems": 

RAStatement: Retrival_Contect_Statement
Retrieval_Context TTOC_Clause DBase_Clause
Retrieval_Statement: Find_Entity_Clause Retrieval_Constraints_Clause
Find_Entity_Clause : Find Retrieval_Scope OF Retrieval_Entities
Retrieval_Entities: Expression | STATISTIC '(' Expression ')' | Expression ',' Retrieval_Entities | STATISTIC '(' Expression Retrieval_Entities
Retrieval_Scope: ALL | ALL_DISTINCT | NONE_ZERO
Retrieval_Constraints_Clause: [Patient_Clause][MLCT_Clause]
MLCT_Clause: MLC_Clause [Temporal_ Expression]
MLC_Clause: [Medical_Constraint_Clause] [Location_Careprovider_Clause]
Location_Careprovider_Clause: [Hospital_Location_Clause][Careprovider_Clause]

 

As a specialist in NLP, she has conducted research on various topics, such as sentiment analysis, topic modeling, and named entity recognition, using machine learning-based, deep learning based, and new-arising transformer-based (BERT, ALBERT, etc.) methods.

As the first author, she has published in leading biomedical informatics journals such as Journal of Biomedical Informatics, Journal of Intelligent Information Systems, and mainstream informatics conferences such as the IASTED International Conference on Biomedical Engineering (BioMed 2013) and 35th Annual International Conference of the IEEE EMBS.

Currently, she is an Assistant Professor at the University of Zanjan, Iran, where she pursues her research in NLP and having some attempt to link it to Bioinformatics domain. Particularly, with collaboration with one of her colleagues (Dr. Alireza Khanteymoori), who is an expert in Bioinformatics, she is currently supervising two PhD students and a master's student in two topics: RNA degradation and CRISPR-based genome editing, aiming to deploy NLP techniques in these two valuable bio-projects. Moreover, she has supervised more than 40 graduate students with a focus on NLP tasks.

Education

Leila holds a Master's degree in Software Engineering from the University of Shahid Beheshti in Tehran, Iran, and a Bachelor's degree in Software Engineering from Sharif University of Technology, which is considered the best engineering school in Iran. She completed her high school education at Farzanegan Talented High School in Zanjan, Iran.

Work Experience

She has worked as an Analyst and Chief Programmer at Informatics Services software company(2003) and Dadevarzi Jame Pardaz software company in Tehran, Iran (2001). She also has worked with Professor Jon Patrick at Innovative Clinical Information Management Systems (iCIMS, Australia’s award-winning cancer informatics solutions) in developing some softwares that links backend NLP solutions into a user-friendly CISs Interfaces, so as to clinical specialist can use them for Data Analytics and Question Answering purposes.


Languages

Leila is fluent in English, Turkish, Persian, and Arabic.

Interests

Leila has broad interests in Machine Learning, Deep Learning, Natural Language Processing (NLP), Information Retrieval, and Text Mining in General and Medical Domains.

Keywords

Knowledge Discovery, Natural Language Processing Health Informatics, Biomedical Informatics, Clinical Data Analytics, Transformers.

Locations

Homepage:  https://leilasafari.com

Location: Department of Computer & Electronic Engineering, University of Zanjan, Zanjan, Iran.

ORCID ID: 0000-0002-2872-0937

 

leila safari