Md Shakhawat Hossain, PhD

Image Processing and Machine Learning researcher with more than 8 years of experience. MY research experiences mainly root in Computational Pathology, Image Processing and Machine Learning. Currently, working as the Head of Medical Imaging and AI research wing at RIoT Lab. My doctoral research was a collaboration between Memorial Sloan Kettering Cancer Center, USA and Tokyo Institute of Technology, Japan. I worked as a Research Scientist at Memorial Sloan Kettering Cancer Center, USA. Received an offer to join Department of Engineering Science at Oxford University, UK as a Senior Researcher of Machine Learning in Medical Imaging. Also worked with the Tokyo Institute of Technology of Japan, Harvard Medical School of USA and Massachusetts General Hospital of USA during my master's program. An inspirational teacher, proactive researcher and effective collaborator. Have more than 4 years of experience in teaching. Proven track records of delivering automated image analysis and diagnosis systems for hospitals. Specialized in statistical model building. Recently, my work is focused on unravelling the role of the HER2 gene in the growth of different cancers such as breast, colon and gastric.

Doctor of Engineering (Oct 2017–Sep 2020)    

School of Engineering, Tokyo Institute of Technology, Japan (in collaboration with Memorial Sloan Kettering Cancer Center,  USA)

Dissertation title: Quality management of whole slide images for the purpose of automatic analysis and diagnosis

Master’s in Engineering (Oct 2015–Sep 2017)

School of Engineering, Tokyo Institute of Technology, Japan (in collaboration with Massachusetts General Hospital, USA and Harvard Medical School, USA)

Dissertation title: Automatic failure detection of whole slide imaging scanner

Master’s in Science (Sep 2011–Sep 2013)

Department of Computer Science and Engineering

School of Engineering, University of Rajshahi, Bangladesh

Dissertation title: Multiband approach for image quality enhancement using Wavelet

Bachelor’s in Science (Feb 2007–Sep 2011)

Department of Computer Science and Engineering

School of Engineering, University of Rajshahi, Bangladesh

Dissertation title: Web-based image processing and enhancement system 

Assistant Professor (Feb 2023 – till date)
Independent University Bangladesh, Dhaka, Bangladesh

Assistant Professor (May 2021 – Feb 2023)
American International University- Bangladesh, Dhaka, Bangladesh

Research Scientist (Sep 2020 – May 2021) 
Memorial Sloan Kettering Cancer Center, New York, USA

Graduate Researcher (Jan 2019 - July 2020) 
Memorial Sloan Kettering Cancer Center, New York, USA

Research Assistant (Aug 2020 - Sep 2020) 
New Energy and Industrial Technology Development Organization (NEDO), Tokyo, Japan (via Tokyo Institute of Technology)

Research Assistant (June - Sep 2018) 
Memorial Sloan Kettering Cancer Center, New York, USA

Research Assistant (Aug 2017-Feb 2018) 
edX, USA (via Tokyo Institute of Technology)

Lecturer (Sep 2013 – Sep 2015) 
ZH Sikder University of Science and Technology, Dhaka, Bangladesh

Software Developer (May - Dec 2012) 
RajIT Software, Rajshahi, Bangladesh 

1.Research Grant for Low-cost and Rapid Breast Cancer Diagnosis in Bangladesh from the Govt. of the People's Republic of Bangladesh (Ministry Of Education), Bangladesh 2023 

2.Warren Alpert Foundation Fellowship, USA 2020 (fund for Postdoctoral Research)

3. Representative Doctoral Student of School of Engineering, Tokyo Tech, Japan 2020

4. Japan Science and Technology (JST) Mirai Grant (in-part), Japan 2020

5. Pathology Informatics Award, USA 2019

6. Research and Education Consortium for Innovation of Advanced Integrated Science (CIAiS) Grant, Japan 2019

7. Japan Science and Technology (PRESTO) Grant (in-part), Japan 2018

8. MURATA Science Foundation Research Grant, Japan 2018

9. JAPAN GOVT. Scholarship (MEXT) for master’s Research (Oct 2015- Sep 2017)

10. JAPAN GOVT. Scholarship (MEXT) for PhD Research (Oct 2017- Sep 2020)

11. 2^ndPosition, Divisional Mathematics Olympiad Bangladesh 2004

12. 4^thPosition, University Day Programming Contest, RUET, Bangladesh 2004

1. Hossain M. Shakhawat, Galib. M.S., Syeed, M. M., Uddin, M. F., Hasan. M., S. Shivam., & S. Advani. (2023). Region of Interest (ROI) Selection using Vision Transformer for Automatic Analysis using Whole Slide Images. Scientific Reports (Nature), vol. 13, 2023, 1038/s41598-023-38109-6.
   
   
2. Hossain M. Shakhawat, Galib. M.S., Syeed, M. M., Uddin, M. F., Hasan. M., Hossain. M.S., & Bari.  R. (2023). Tissue Artifact Segmentation and Severity Assessment for Automatic Analysis using WSI. IEEE Access, vol. 11, pp. 21977-21991, 2023, doi: 10.1109/ACCESS.2023.3250556.
   
   
3. Hossain M. Shakhawat, Mahmudur R., Syeed, M. M., Uddin, M. F., Hasan. M., Hossain. M.S., & others (2023). DeepPoly: Deep Learning-based Polyps Segmentation and Classification for Autonomous Colonoscopy Examination. IEEE Access, vol. 11, pp. 95889-95902, 2023, doi:10.1109/ACCESS.2023.3310541.
   
   
4. Hossain M. Shakhawat, Matthew Hanna, Naohiro Uraoka, Tomoya Nakamura, Marcia Edelweiss, Edi Brogi, Meera R. Hameed, Masahiro Yamaguchi, Dara S. Ross, Yukako Yagi (2019). Automatic  quantification of HER2 gene amplification in invasive breast cancer from chromogenic in situ hybridization whole slide images. SPIE Journal of Medical Imaging, 6(4), 047501, https://doi.org/10.1117/1.JMI.6.4.047501, PubMed PMID: 31763355
   
   
5. Hossain M. Shakhawat, Tomoya Nakamura, Fumikazu Kimura, Yukako Yagi, Masahiro Yamaguchi (2020). Automatic quality evaluation of whole slide images for the practical use of whole slide imaging scanner. ITE Trans. On MTA Vol. 8, No.4, pp. 252-268. https://doi.org/10.3169/mta.8.252
   
   
6. Hossain M. Shakhawat, Syeed, M. M., Fatema, K., Hossain, M. S., & Uddin, M. F. (2022). Singular Nuclei Segmentation for Automatic HER2 Quantification Using CISH Whole Slide Images. Sensors, 22(19), 7361, doi: 10.3390/s22197361. PubMed PMID: 36236459
   
   
7. Hossain M. Shakhawat, Syeed, M. M., Fatema, K., & Uddin, M. F. (2022). The Perception of Health Professionals in Bangladesh toward the Digitalization of the Health Sector. International Journal of Environmental Research and Public Health, 19(20), 13695, doi: 10.3390/ijerph192013695, PubMed PMID: 36294274
   
   
8. Hossain M. S., Hasan. N., Samad, M. A., & Hossain M. Shakhawat, Karmoker J., Ahmed. F., Fuad. N., Choi. K. (2022). Android Ransomware Detection from Traffic Analysis Using Metaheuristic Feature Selection", IEEE Access, , vol. 10, pp. 128754-128763, 2022, doi: 10.1109/ACCESS.2022.3227579.
   
   
9. Hossain M. Shakhawat, Raihan, M. E., Hossain, M. S., Syeed, M. M., Rashid, H., & Reza, M. S. (2022). Aedes Larva Detection using Ensemble Learning to Prevent Dengue Endemic. BioMedInformatics, Vol2,3,pp.405-423
   
   
10. Syed M. M. M.,Hossain M. Shakhawat, Karim, M. R., Uddin, M. F., Hasan. M., & R. H. Khan.  R. (2023). Surface water quality profiling using the water quality index, pollution index and statistical methods: A critical review. Environmental and Sustainability Indicators, vol. 18, pp. 100247, 2023, https://doi.org/10.1016/j.indic.2023.100247.
    
    
11. Hossain M.S. et al. (2023), Adoption of Unmanned Aerial Vehicle (UAV) imagery in agricultural management: A systematic literature review, Ecological Informatics (Elsevier)