Experience

Research Fellow   Beth Israel Deacones Medical Center, Harvard Medical School, MA USA      Mar, 2014 - Current

• • Advanced a novel computational system to discriminate expanded images of early stage breast neoplastic lesions (Expansion Pathology) which significantly improve cancer diagnostics (Nature Biotechnology 2017). Patent application is submitted.

  • Developed a crowdsourcing based image classification technique for stratification of protein expression in immunohistochemistry images (TMAs) and evaluated with automated method and expert labels (Nature Scientific Reports 2017). 

  • Won the Camelyon 2016 contest of cancer detection (ISBI 2016). The CNN model was applied to generate tumor prediction heatmaps, which were then used to extract geometric features and trained a random forest to estimate the cancer probability.

  • Proposed a computational framework to identify the association of histologic features with diagnostic concordance among pathologists and identify cases for referral for a second opinion/external review (USCAP 2016).

  • Designed 3D computational platforms including rapid image acquisition, nuclei segmentation, feature computation and classification of normal, pre-invasive and invasive breast cases (AACR 2015).

  • Developed crowdsourcing based annotation application for nuclei detection and segmentation in pathological images (PSB 2015).

  • Advanced a computational framework to segment nuclei, compute nuclei features and classify histopathological images into benign (UDH) and pre-invasive (DCIS) breast cases (PlosOne 2014).

  • Programming Languages: Python, Matlab, R, TensorFlow, ImageJ, Fiji, Weka, Java, ITK.

Research Engineer   IPAL UMI CNRS I2R A*STAR, Singapore                                                       Nov, 2010 - Feb, 2014

• I am working on MICO – Cognitive Virtual Microscopy funded by French National Research Agency ANR under reference ANR-10-TECS-015. My work includes automated mitosis detection in color and multispectral images of breast cancer histopathology. I have developed an efficient and generic strategy to explore large images, like WSI, by combining computational geometry tools with a local signal measure of relevance in dynamic sampling framework. The real time evaluations of these methods are done in MICO platform at Pitié-Salpêtrière Hospital (GHU-PS) Paris, France. By being part of a team which has industrial partners, breast cancer grading is developed, tested and validated in the frame of project MICO in order to demonstrate the viability and relevance of the system.

• I am also working on discrete geometry data structure and algorithm for 2-manifolds (meshes) in ITK under the supervision of Alexandre Gouaillard (member of Editorial Committee - ITK Consortium).

• Programming Languages: C++, ITK, VTK, Matlab, Java, ImageJ, Weka, CMake, GIT.

Research Engineer   nexGIN RC NUCES Islamabad Pakistan                                                       Feb, 2009 – Aug, 2010

• I worked on a research project titled “Remote Patient Monitoring System (RPMS)”. The primary goal of this project was to design a generic remote health care system with a focus on antenatal care that enhances services provided by health workers and doctors. This project won the World Summit Youth Award 2009 out of 612 participant projects. It was a runner up for P@sha ICT Award 2009 in research and development category.

• My responsibility included the development of electronic medical record (EMR), web server, mobile and web applications and SMS based notification system between doctors and health workers. I also developed hybrid decision support system having case based reasoning and machine learning technique (Decision Tree C4.5), which helped in diagnosis, medications and treatments.

• I also worked on an offshoot of RPMS project, ultrasound anomalies detection using image processing and AI techniques.

• Programming Languages: Java, J2ME, JSP, J2EE, MySql, Weka, Matlab, Tomcat Server, Netbeans.

Software Engineer                Cogilent Solutions, Pakistan                                                           Mar, 2008 – Jan, 2009

• Cogilent Solutions is a product base company which has many products like BrightSpyre (HR Solution), PersonForce, Web Portals and JobBoards. My responsibilities were requirement analysis, design & development of new web portals and affiliates and also maintenance of running products (BrightSpyre, JobBoards, PersonForce).

• Programming Languages: PHP, MySql, CSS, Ajax, Javascript, Eclipse, Apache Server.

Teaching Assistant               NUCES-FAST Islamabad, Pakistan                                                Feb, 2007 – Feb, 2008

• I assisted professors in execution of the courses including grading, weekly lab sessions, providing consultations to students and managing students’ projects for database management system, computer programming, data structure and algorithms.

Teaching Assistant               GIK Institute Topi, Pakistan                                                          Jan, 2006 – Aug, 2006

• I assisted professors in execution of the database management system course including grading, weekly lab sessions, providing consultations to students and managing students’ projects.

Software Engineer                RIDOS Solutions Pakistan                                                            Jan, 2005 – Aug, 2006

• RIDOS solutions is a software development company that has different solutions for accounting, sale, purchase, stock and production systems. My responsibilities were clarifying software requirements, design and development of systems.

• Programming Languages: VC++, VB, Visual Studio 2005, Sql Server, Oracle 9i, Developer.