Middle East Technical University

Computer Engineering - PhD • September 2012 - November 2018

My PhD studies was related to personalization of just-in-time adaptive interventions that are employed to help individuals in their self-management activities to cope with their health problems or chronic diseases. The study presents a reinforcement learning-based algorithm adapting the intervention delivery in terms of type, frequency and timing of interventions. The proposed algorithm is validated via a simulated-based case study.

Middle East Technical University

Computer Engineering - MSc • September 2010 - July 2012

The main aim of my graduate studies was to enhance legacy content management systems with features considering semantics of managed content. Inline with this aim, I've built an integrative system realizing 1) content retrieval from legacy content management systems, 2) enhancing content with domain-specific semantic annotations, 3) storing semantic annotations in dedicated indices, which are one-to-one compatible with the structure of domain-specific semantic annotations. The system described above was implemented in the scope of Apache Stanbol.

Middle East Technical University

Computer Engineering - BSc • September 2005 - July 2010

In addition to computer science and engineering, my undergraduate education was rather focused on software engineering field. Taking also my graduate and doctorate education into account, I took approximately 40 courses related with those fields among which I see the followings ones as most important: "Operating Systems", "Algorithms", "Computer Organization", "Software Engineering", "Theory of Computation", "Programming Languages", "File Systems", "Database Management Systems", "Data Mining" and "Statistical Data Analysis".

SRDC

Researcher• October 2014 - Present

As a researcher I've involved in and worked on all phases of proposal preparation in the scope of European Commission's FP7 and H2020 programs. I have mainly took part in projects from manufacturing and eHealth domains.

In the manufacturing domain, I was one of the main writers of the NIMBLE Project. In NIMBLE, I have worked on merging eCommerce and B2B collaboration platforms for increasing visibility of SMEs serving in industry in some way and help them to achieve their goals faster and at a lower cost.

In the eHealth domain, I've participated in research on the design of decision support system for patients with chronic cardio-respiratory diseases integrated with real-time telemonitoring system. The decision support system was supposed to prevent exacerbations via predictive and probabilistic modeling on prognosis of diseases.

Further in the eHealth domain, I've involved in design of a system (i.e SALUS Project) aiming to utilization of electronic health records (EHR) aggregated in hospitals or similar clinical care organizations in drug post market safety studies. Together with my colleagues, we've designed methodologies for semantic and functional interoperability among various clinical information systems, content models and clinical terminologies.

SRDC

Software Engineer• October 2008 - Present

As a software engineer in SRDC, I've designed and developed modular, service oriented applications as well as large-scale software infrastructures composed of several components. I've undertaken team-lead and software architect roles as well as involving in the development activities myself. As I worked on both user-interface and background software modules during the course of these projects, I was able to gain skills on various client-side and server-side technologies.I've worked in large-scale R&D projects, from different domains with different research focuses, as listed below:

• iSurf (manufacturing, supply chain management, eBusiness interoperability)
• IKS (semantic web, semantic content management, semantic enrichment, semantic search & indexing)
• Salus (eHealth, semantic interoperability, post market safety studies on EHR, clinical terminology interoperability)
• NIMBLE (B2B collaboration, eCommerce, business processes, semantic product definitions, product classification taxonomies)

Apache Software Foundation

Committer• March 2011 - Present

I'm a committer for Apache Stanbol. The main aim of Stanbol is to develop modular content enrichment services; using semantic, linguistic and lexical technologies, which could be used as external services or as embedded components by legacy content management systems. My role in Stanbol was to implement services for managing the produced semantic enhancements without losing semantic meaning and context awareness. In addition to storage functionalities based on different storage and indexing infrastructures including Apache Solr and Apache Jena, I implemented semantic search functionalities considering the relations between words/concepts coded in different lexical ontologies including WordNet or other domain-specific ontologies.

Middle East Technical University

Student Assistant• September 2007 - June 2008

I was a student assistant in Computer Engineering Department during two semesters. I was organizing laboratory exams and preparing questions for these exams in the scope of a programming language course enrolled by other engineering students.

Dissertations

Suat Gönül A Framework for Design and Personalization of Digital, Just-In-Time, Adaptive InterventionsMiddle East Technical University - Computer Engineering Department

Suat Gönül Enhancing Content Management Systems with Semantic CapabilitiesMiddle East Technical University - Computer Engineering Department

Journal Papers

Suat Gonul, Tuncay Namli, Ismail Hakki Toroslu, Ahmet Cosar A Reinforcement Learning Based Algorithm for Personalization of Digital, Just-In-time, Adaptive InterventionsApplied Intelligence

Suat Gonul, Tuncay Namli, Sasja Huisman, Gokce Banu Laleci Erturkmen, Ismail Hakki Toroslu, Ahmet Cosar An Expandable Approach for Design and Personalization Digital, Just-In-Time, Adaptive InterventionsJournal of the American Medical Informatics Association, November 2018

Anil Pacaci, Suat Gonul, A. Anil Sinaci, Mustafa Yuksel, Gokce B. Laleci Erturkmen A Semantic Transformation Methodology for the Secondary Use of Observational Healthcare Data in Postmarketing Safety StudiesFrontiers in Pharmacology, 9, April, 2018

Mustafa Yuksel, Suat Gonul, Gokce B. Laleci Erturkmen, Ali Anil Sinaci, Paolo Invernizzi, Sara Facchinetti, Andrea Migliavacca, Tomas Bergvall, Kristof Depraetere, Jos De Roo An Interoperability Platform Enabling Reuse of Electronic Health Records for Signal Verification StudiesBioMed Research International, March, 2016

A. Anil Sinaci, Gokce B. Laleci Erturkmen, Gonul S., Mustafa Yuksel, Paolo Invernizzi, Bharat Thakrar, Anil Pacaci, H. Alper Cinar, Nihan Kesim Cicekli Postmarketing Safety Study Tool: A Web Based, Dynamic, and Interoperable System for Postmarketing Drug Surveillance StudiesBioMed Research International, May, 2015

Conference Papers

Suat Gonul, Tuncay Namli, Mert Baskaya, A. Anil Sinaci, Ahmet Cosar, Ismail Hakki Toroslu Optimization of Just-in-Time Adaptive Intervension Using Reinforcement LearningIn International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems , June, 2018, Montreal, Canada

Quan Deng, Suat Gonul, Yildiray Kabak, Nicola Gessa, Dietmar Glachs, Fernando Gigante, Violeta Damjanovic-Behrendt, Karl Hribernik, Klaus-Dieter Thoben An Ontology Framework for Multisided Platform InteroperabilityIn 9th International Conference on Interoperability for Enterprise Systems and Applications (I-ESA 2018), March, 2018, Berlin, Germany

Johannes Innerbichler, Suat Gonul, Violeta Damjanovic-Behrendt, Benjamin Mandler, Felix Strohmeier NIMBLE collaborative platform: Microservice architectural approach to federated IoTIn Global Internet of Things Summit (GIoTS), June, 2017, Montreal, Canada

Tobias Krahn, Marco Eichelberg, Frerk Müller, Suat Gonul, Gokce B. Laleci Erturkmen, A. Anil Sinaci, H.-Jürgen Appelrath Adverse Drug Event Notification on a Semantic Interoperability FrameworkIn MIE 2014, August 31 - September 02, 2014, Istanbul, Turkey (Rolf Hansen Memorial Award - The best paper on electronic health records)

A. Anil Sinaci, Gokce B. Laleci Erturkmen, Suat Gonul, H. Alper Cinar, Atakan Kaya Patient History Navigation with the Use of Common Data ElementsIn International Workshop on Semantic Web Applications and Tools for Life Sciences, SWAT4LS, December, 2013, Edinburgh, Scotland

Mustafa Yuksel, Suat Gonul, Gokce Banu Laleci Erturkmen, Ali Anil Sinaci, Kristof Depraetere, Jos De Roo, Tomas Bergvall Demonstration of the SALUS Semantic Interoperability Framework for Case Series Characterization StudiesIn International Workshop on Semantic Web Applications and Tools for Life Sciences, SWAT4LS, December, 2013, Edinburgh, Scotland

Suat Gonul, Ali Anil Sinaci Semantic Content Management and Integration with JCR/CMIS Compliant Content RepositoriesIn I-Semantics Conference, September, 2012, Graz, Austria

Ali Anil Sinaci, Suat Gonul Semantic Content Management with Apache StanbolIn In Extended Semantic Web Conference (pp. 371-375), May, 2012, Heraklion, Crete, Greece

Tuncer F., Dogac A., Postaci S., Gonul S., Alpay E. iSURF eDoCreator: e-Business Document Design and Customization EnvironmentIn eChallenges Conference, October, 2009, Istanbul, Turkey

Demonstrations/Talks

Ali Anil Sinaci, Suat Gonul Semantic Content Management with Apache StanbolIn ESWC Conference, May, 2012, Heraklion, Crete, Greece

Suat Gonul , Ali Anil Sinaci Semantic Indexing and Search for Content Management Systems with Apache StanbolIn ApacheCon, Linked Data Track, November, 2012, Sinsheim, Germany