Malay SINGH

Research Interests

My current research focuses on applications of image processing, computer vision, machine learning, deep learning, pattern recognition and mathematical modeling in biological and biomedical image analysis and informatics.
I have been developing algorithms for histological tissue images analysis for 11 years. My research includes developing automatic feature extraction and classification methods to solve object detection, object classification and image segmentation problems in histopathological tissue images.

Publications

Journal Publications

  1. Narmada BC*, Khakpoor A*, Shirgaonkar N*, Narayanan S, Kim Aw PP, Singh M, Ong KH, Owino CO, Ting Ng JW, Yew HC, Binte Mohamed Nasir NS, Au VB, Sng R, Kaliaperumal N, Toe Wai Khine HH, Casuscelli di Tocco F, Masayuki O, Naikar S, Ng HX, Chia SL, Yi Seah CX, Alnawaz MH, Lee Yoon Wai C, Ling Tay AY, Singh MK, Chew V, Yu W, Connolly JE, Periyasamy G, Plissonnier ML, Levrero M, Lim SG, DasGupta R.
    Single cell landscape of functionally cured chronic hepatitis B patients reveals activation of innate and altered CD4-CTL-driven adaptive immunity.
    Journal of Hepatology (2024) *Equal contribution. (DOI).

  2. Mustafa Umit Oner*, Mei Ying Ng*, Danilo Medina Giron, Cecilia Ee Chen Xi, Louis Ang Yuan Xiang, Malay Singh, Weimiao Yu, Wing-Kin Sung, Chin Fong Wong, and Hwee Kuan Lee.
    An AI-assisted Tool For Efficient Prostate Cancer Diagnosis in Low-grade and Low- volume Cases.
    Patterns 3 (12), 100642 (2022). *Equal contribution. (Dataset, Code, and PDF).

  3. Bhav Harshad Parikh*, Zengping Liu*, Paul Blakeley, Qianyu Lin, Malay Singh, Jun Yi Ong, Kim Han Ho, Joel Weijia Lai, Hanumakumar Bogireddi, Kim Chi Tran, Jason Y. C. Lim, Kun Xue, Abdurrahmaan Al-Mubaarak, Binxia Yang, Sowmiya R, Kakkad Regha, Daniel Soo Lin Wong, Queenie Shu Woon Tan, Zhongxing Zhang, Anand D. Jeyasekharan, Veluchamy Amutha Barathi, Weimiao Yu, Kang Hao Cheong, Timothy A. Blenkinsop, Walter Hunziker, Gopal Lingam, Xian Jun Loh, and Xinyi Su.
    A bio-functional polymer that prevents retinal scarring through modulation of NRF2 signalling pathway.
    Nature Communications 13, 2796 (2022). *Equal contribution. (PDF).

  4. Daniel Aitor Holdbrook*, Malay Singh*, Yukti Choudhury, Emarene Mationg Kalaw, Valerie Koh, Hui Shan Tan, Ravindran Kanesvaran, Puay Hoon Tan, John Yuen Shyi Peng, Min-Han Tan, and Hwee Kuan Lee.
    Automated renal cancer grading using nuclear pleomorphic patterns.
    JCO Clinical Cancer Informatics 2018 :2, 1-12. *Equal contribution. (PDF).

  5. Oleg V. Grinchuk, Surya Pavan Yenamandra, Ramakrishnan Iyer, Malay Singh, Hwee Kuan Lee, Igor V. Kurochkin, Kiat Hon Lim, Pierce K. H. Chow, and Vladimir A. Kuznetsov.
    Tumor-adjacent tissue co-expression profile analysis reveals pro-oncogenic gene signature for prognosis of resectable hepatocellular carcinoma.
    Molecular Oncology. 12(1):89-113, 2018 (PDF).

  6. Malay Singh, Emarene Mationg Kalaw, Danilo Medina Giron, Kian-Tai Chong, Chew Lim Tan, and Hwee Kuan Lee.
    Gland segmentation in prostate histopathological images.
    Journal of Medical Imaging. 4(2), 027501 (2017), (PDF).

  7. Choon Kong Yap, Emarene Mationg Kalaw, Malay Singh, Kian-Tai Chong, Danilo Medina Giron, Chao-Hui Huang, Li Cheng, Yan Nei Law, and Hwee Kuan Lee.
    Automated Image Based Prominent Nucleoli Detection.
    Journal of Pathology Informatics 6.1 (2015): 39. (PDF)

Conference Posters

  1. Kok Haur ONG, Laurent Gole, Longjie LI, Xinmi HUO, Kah Weng LAU, David M. YOUNG, Susan Swee Shan HUE, Char Loo TAN, Gabriel Pik Liang MARINI, Hao HAN, Malay Singh, Haoda LU, Soo Yong TAN*, Weimiao YU*.
    Digital pathology annotation & image quality assessment platform for developing and training various AI cancer models and realizing the intelligent clinical assessment.
    Poster presentation at HPCAsia2023: International Conference on High Performance Computing in Asia Pacific Region (HPCAsia2023). 27 Feb - 2 March 2023. HPCAsia2023. *Corresponding Authors.

  2. Nicholas Cheng, Eddy W. P. Tan, Shuang Leng, Lohendran Baskaran, Lynette Teo, Min Sen Yew, Malay Singh, Weimin Huang, Mark Yan-Yee Chan, Kee Yuan Ngiam, Roger Vaughan, Terrance Chua, Swee Yaw Tan, Hwee Kuan Lee, Liang Zhong.
    Machine Learning Accurately Quantifies Epicardial Adipose Tissue from non-contrast CT images in Coronary Artery Disease.
    Poster presentation at ESC Asia 2022 with APSC & AFC Conference by European Society of Cardiology. Singapore. December 2022. ESC2022

  3. Malay Singh, Laurent Gole, Kok Haur Ong, Longjie Li, Xinmi Huo, Hao Han, Kah Weng Lau, Li Mei Gan, Char Loo Tan, David M Young, Hwee Kuan Lee, Susan Swee Shan Hue, Weimiao Yu, and Soo Yong Tan.
    Highly multiplexed immuno-fluorescence images data analysis for prostate cancer.
    Poster at "Frontiers in Cancer Science 2021". (FCS2021).

  4. Malay Singh,Laurent Gole, Kok Haur Ong, Hao Han, David M Young, Susan Swee Shan Hue, Soo Yong Tan, and Weimiao Yu.
    Highly multiplexed immuno-fluorescence images data analysis for prostate cancer.
    Poster at "Frontiers in Cancer Science 2020". (FCS2020).

  5. Brandon Ryan Hong, Malay Singh, Jane Vin Chan, Matan Thangavelu, Giridharan Periyasamy, Hwee Kuan Lee, and Judice L. Y. Koh.
    Predicting Drug Response in 3D Tumor Spheroids using Convolutional Neural Networks. Poster at “EMBL Symposium: Seeing is Believing - Imaging the Process of Life”. EMBL Heidelberg, Germany. October 2017.

Conference Articles

  1. Malay Singh, Zeng Zeng, Emarene Mationg Kalaw, Danilo Medina Giron, Kian-Tai Chong, and Hwee Kuan Lee.
    A study of nuclei classification methods in histopathological images.
    International Conference on Innovation in Medicine and Healthcare, (KES-InMed-17), (SpringerLink).

  2. Malay Singh,Uma Shanker Tiwary, and Tanveer J. Siddiqui.
    A speech retrieval system based on fuzzy logic and knowledge-base filtering.
    In International Conference on Multimedia, Signal Processing and Communication Technologies (IMPACT), 2013 , pp. 46-50. IEEE, 2013. (IEEEXplore)

  3. Anupam Srivastava, Divij Vaidya, Malay Singh, Pranjal Singh, and Uma Shanker Tiwary.
    A cognitive interactive framework for multi-document summarizer.
    Advances in Intelligent Systems and Computing, 1, Volume 179, Proceedings of the Third International Conference on Intelligent Human Computer Interaction (IHCI 2011), Prague, Czech Republic, August, 2011, Part 5, Pages 257-268. (PDF), ( SpringerLink)

Seminars and Talks

  1. Invited seminar in the AI DP Informatics Journal Club at SGH. Using Deep Learning to Assist Pathologists in Prostate Cancer Grading. Online. 20 June 2023.

  2. Invited talk at Digital Pathology Malaysia 2023 Conference. Using Deep Learning to Assist Pathologists in Prostate Cancer Grading. Kuala Lumpur, Malaysia. 27 June 2023.

  3. Invited talk at Unlocking the Power of Spatial Omics Symposium. Structure Based Immune Profiling Using Multiplex Immunofluorescence Images for Prostate Cancer. Singapore. 5 October 2023.

  4. Invited talk at Department of Pathology, Erasmus Medical Center (EMC), The Netherlands. Using Deep Learning to Assist Pathologists in Prostate Cancer Grading. Online. 17 November 2023.

  5. Invited seminar in the AI DP Informatics Journal Club at SGH. AI driven tool to analyse intra-tumor heterogeneity for patient prognosis Online. 1 Oct 2024.

    6. Talks (1-2 and 4 above) were an abridged version of the Cell Patterns paper: Oner et al. 2022 Patterns.

Preprints

  1. Malay Singh, Emarene Mationg Kalaw, Wang Jie, Mundher Al-Shabi, Chin Fong Wong, Danilo Medina Giron, Kian-Tai Chong, Maxine Tan, Zeng Zeng, and Hwee Kuan Lee.
    Cribriform pattern detection in prostate histopathological images using deep learning models.
    arXiv, 1910.04030. (PDF).

Internships

  1. MITACS Globalink Research Internship 2011 at Department of Chemical & Materials Engineering,University of Alberta.
    We implemented a model of oil reservoirs using MATLAB. We tried to infer a relation between Well location and migration of CO2 in depleted or near-depleted oil reservoirs. We aimed to optimize the amount of Carbon Dioxide injected into the reservoir within the constraints of Parameters like Bottom Hole Pressure, Permeability and Porosity of Rocks.

malay.1989@gmail.com