University of Waterloo

M. Javad Shafiee

Research Assistant Professor

I am a Research Assistant Professor in the Department of Systems Design Engineering at University of Waterloo under the supervision of Prof. Alexander Wong. I received my Ph.D. under supervision of Prof. Alexander Wong and Prof. Paul Fieguth. My Bachelor’s degree is in Computer Science and Engineering from Shiraz University in Iran in 2008 and I received my my master degree in Artificial Intelligent in 2011 from same university.

Currently, I am working on efficient deep learning methods for embedded systems with application on autonomous driving cars, traffic monitoring and healthcare. 

My PhD thesis topic was about introducing a “Randomly-connected Non-Local Conditional Random Fields” to address long-range spatial connectivity while maintaining computational complexity. 

My master thesis was focused on A Novel Conditional Random Field Framework For Object Tracking supervised by Prof. Zohreh Azimifar.

Research interests
My research interests include Computer Vision, Machine Learning and Biomedical Image Processing which my main focus is on Graphical Models especially Deep Learning, Conditional Random Fields and Markov Random Fields.
Publications
Journal Articles

Aboutalebi H., Shafiee M.J., Tai C.-E.A., and Wong A, "Knowing is Half the Battle: Enhancing Clean Data Accuracy of Adversarial Robust Deep Neural Networks via Dual-Model Bounded Dive", IEEE Access, vol. 12, pp. 48174-48188, 2024. Get it here. Aboutalebi H., Pavlova M., Shafiee M.J., Sabri A., Alaref A., and Wong A, "COVID-net CXR-S: Deep convolutional neural network for severity assessment of COVID-19 cases from chest X-ray images", Diagnostics, vol. 12, 2022. Get it here. Aboutalebi H., Pavlova M., Gunraj H., Shafiee M.J., Sabri A., Alaref A., and Wong A, "MEDUSA: Multi-Scale Encoder-Decoder Self-Attention Deep Neural Network Architecture for Medical Image Analysis", Frontiers in Medicine, vol. 8, 2022. Get it here. Shafiee M.J., Jeddi A., Nazemi A., Fieguth P., and Wong A, "Deep Neural Network Perception Models and Robust Autonomous Driving Systems: Practical Solutions for Mitigation and Improvement", IEEE Signal Processing Magazine, vol. 38, pp. 22-30, 2021. Get it here. Abbasi S., Famouri M., Shafiee M.J., and Wong A, "Outliernets: Highly compact deep autoencoder network architectures for on-device acoustic anomaly detection", Sensors, vol. 21, 2021. Get it here. Nazemi A., Azimifar Z., Shafiee M.J., and Wong A, "Real-Time Vehicle Make and Model Recognition Using Unsupervised Feature Learning", IEEE Transactions on Intelligent Transportation Systems, vol. 21, pp. 3080-3090, 2020. Get it here. Wong A., Shafiee M.J., Chwyl B., and Li F, "Gensynth: A new way to understand deep learning", Electronics Letters, vol. 55, pp. 970-971, 2019. Get it here. Wong A., Shafiee M.J., Chwyl B., and Li F, "Gensynth: A generative synthesis approach to learning generative machines for generate efficient neural networks", Electronics Letters, vol. 55, pp. 986-989, 2019. Get it here. Shafiee M.J., Chwyl B., Li F., Chen R., Karg M., Scharfenberger C., and Wong A, "StressedNets: Efficient feature representations via stress-induced evolutionary synthesis of deep neural networks", Neurocomputing, vol. 127, pp. 93-105, 2019. Get it here. Khalvati F., Zhang J., Chung A.G., Shafiee M.J., Wong A., and Haider M.A, "MPCaD: A multi-scale radiomics-driven framework for automated prostate cancer localization and detection", BMC Medical Imaging, vol. 18, 2018. Get it here. Shafiee M.J., Siva P., Fieguth P., and Wong A, "Real-Time Embedded Motion Detection via Neural Response Mixture Modeling", Journal of Signal Processing Systems, vol. 90, pp. 931-946, 2018. Get it here. Shafiee M.J., Mishra A., and Wong A, "Deep Learning with Darwin: Evolutionary Synthesis of Deep Neural Networks", Neural Processing Letters, vol. 48, pp. 603-613, 2018. Get it here. Wong A., Shafiee M.J., and St Jules M, "MicronNet: A highly compact deep convolutional neural network architecture for real-time embedded traffic sign classification", IEEE Access, vol. 6, pp. 59803-59810, 2018. Get it here. Shafiee M.J., Chung A.G., Khalvati F., Haider M.A., and Wong A, "Discovery radiomics via evolutionary deep radiomic sequencer discovery for pathologically proven lung cancer detection", Journal of Medical Imaging, vol. 4, 2017. Get it here. Shafiee M.J., Wong A., and Fieguth P, "Deep Randomly-Connected Conditional Random Fields for Image Segmentation", IEEE Access, vol. 5, pp. 366-378, 2017. Get it here. Ben Daya I., Chen A.I.H., Shafiee M.J., Wong A., and Yeow J.T.W, "Compensated Row-Column Ultrasound Imaging System Using Multilayered Edge Guided Stochastically Fully Connected Random Fields", Scientific Reports, vol. 7, 2017. Get it here. Xu L., Shafiee M.J., Wong A., and Clausi D.A, "Fully Connected Continuous Conditional Random Field with Stochastic Cliques for Dark-Spot Detection in SAR Imagery", IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, vol. 9, pp. 2882-2890, 2016. Get it here. Shafiee M.J., Siva P., Scharfenberger C., Fieguth P., and Wong A, "NeRD: A Neural Response Divergence Approach to Visual Saliency Detection", IEEE Signal Processing Letters, vol. 23, pp. 1404-1408, 2016. Get it here. Boroomand A., Shafiee M.J., Khalvati F., Haider M.A., and Wong A, "Noise-Compensated, Bias-Corrected Diffusion Weighted Endorectal Magnetic Resonance Imaging via a Stochastically Fully-Connected ", IEEE Transactions on Medical Imaging, vol. 35, pp. 2587-2597, 2016. Get it here. Beltrame T., Amelard R., Villar R., Shafiee M.J., Wong A., and Hughson R.L, "Estimating oxygen uptake and energy expenditure during treadmill walking by neural network analysis of easy-to-obtain inputs", Journal of Applied Physiology, vol. 121, pp. 1226-1233, 2016. Get it here. Li E., Khalvati F., Shafiee M.J., Haider M.A., and Wong A, "Sparse reconstruction of compressive sensing MRI using cross-domain stochastically fully connected conditional random fields", BMC Medical Imaging, vol. 16, 2016. Get it here. Haider S.A., Cameron A., Siva P., Lui D., Shafiee M.J., Boroomand A., Haider N., and Wong A, "Fluorescence microscopy image noise reduction using a stochastically-connected random field model", Scientific Reports, vol. 6, 2016. Get it here. Li E., Shafiee M.J., Kazemzadeh F., and Wong A, "Sparse Reconstruction of Compressive Sensing Multi-Spectral Data Using an Inter-Spectral Multi-Layered Conditional Random Field ", IEEE Access, vol. 4, pp. 5540-5554, 2016. Get it here. Shafiee M.J., Siva P., and Wong A, "StochasticNet: Forming Deep Neural Networks via Stochastic Connectivity", IEEE Access, vol. 4, pp. 1915-1924, 2016. Get it here. Chung A.G., Khalvati F., Shafiee M.J., Haider M.A., and Wong A, "Prostate cancer detection via a quantitative radiomics-driven conditional random field framework", IEEE Access, vol. 3, pp. 2531-2541, 2015. Get it here. Shafiee M.J., Haider S.A., Wong A., Lui D., Cameron A., Modhafar A., Fieguth P., and Haider M.A, "Apparent ultra-high b-value diffusion-weighted image reconstruction via hidden conditional random fields", IEEE Transactions on Medical Imaging, vol. 34, pp. 1111-1124, 2015. Get it here. Daya I.B., Chen A.I.H., Shafiee M.J., Wong A., and Yeow J.T.W, "Compensated Row-Column Ultrasound Imaging System Using Fisher Tippett Multilayered Conditional Random Field Model", PLoS ONE, vol. 10, 2015. Get it here. Shafiee M.J., Azimifar Z., Wong A., and Wang Y, "A deep-structured conditional random field model for object silhouette tracking", PLoS ONE, vol. 10, 2015. Get it here. Wong A., Shafiee M.J., Siva P., and Wang X.Y, "A deep-structured fully connected random field model for structured inference", IEEE Access, vol. 3, pp. 469-477, 2015. Get it here. Wong A., Shafiee M.J., and Azimifar Z, "Statistical Conditional Sampling for Variable-Resolution Video Compression", PLoS ONE, vol. 7, 2012. Get it here. Aboutalebi H., Pavlova M., Shafiee M.J., Florea A., Hryniowski A., and Wong A, "COVID-Net Biochem: an explainability-driven framework to building machine learning models for predicting survival and kidney inj", Scientific Reports, vol. 13, 2023. Get it here. Lu D., Schwartz S., Xu L., Shafiee M.J., Vinson N.G., Czarnecki K.J., and Wong A, "Integrating deep transformer and temporal convolutional networks for SMEs revenue and employment growth prediction", Expert Systems with Applications, vol. 127, . Get it here.

Conference Papers

Wong A., Wu Y., Abbasi S., Nair S., Chen Y., and Shafiee M.J, "Fast GraspNeXt: A Fast Self-Attention Neural Network Architecture for Multi-task Learning in Computer Vision Tasks for Robotic G", IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops, 2023. Get it here. Jeddi A., Shafiee M.J., Karg M., Scharfenberger C., and Wong A, "Learn2Perturb: An end-to-end feature perturbation learning to improve adversarial robustness", Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2020. Get it here. Boroomand A., Tan B., Shafiee M.J., Bizheva K., and Wong A, "A random field computational adaptive optics framework for optical coherence microscopy", Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2019. Get it here. Shafiee M.S., Shafiee M.J., and Wong A, "Dynamic representations toward efficient inference on deep neural networks by decision gates", IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops, 2019. Get it here. Daya I.B., Shafiee M.J., Karg M., Scharfenberger C., and Wong A, "SANE: Towards improved prediction robustness via stochastically activated network ensembles", IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops, 2019. Get it here. Daya I.B., Shafiee M.J., Karg M., Scharfenberger C., and Wong A, "SANE: Exploring adversarial robustness with stochastically activated network ensembles", IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops, 2019. Get it here. Wong A., Famuori M., Shafiee M.J., Li F., Chwyl B., and Chung J, "YOLO Nano: A Highly Compact You only Look Once Convolutional Neural Network for Object Detection", Proceedings - 5th Workshop on Energy Efficient Machine Learning and Cognitive Computing, EMC2-NIPS 2019, 2019. Get it here. Wong A., Shafiee M.J., Li F., and Chwyl B, "Tiny SSD: A tiny single-shot detection deep convolutional neural network for real-time embedded object detection", Proceedings - 2018 15th Conference on Computer and Robot Vision, CRV 2018, 2018. Get it here. Chwyl B., Chung A.G., Shafiee M.J., Fu Y., and Wong A, "DeepPredict: A deep predictive intelligence platform for patient monitoring", Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS, 2017. Get it here. Chung A.G., Shafiee M.J., Fieguth P., and Wong A, "The Mating Rituals of Deep Neural Networks: Learning Compact Feature Representations Through Sexual Evolutionary Synthesis", Proceedings - 2017 IEEE International Conference on Computer Vision Workshops, ICCVW 2017, 2017. Get it here. Karimi A.-H., Chung A.G., Shafiee M.J., Khalvati F., Haider M.A., Ghodsi A., and Wong A, "Discovery radiomics via a mixture of deep ConvNet sequencers for multi-parametric MRI prostate cancer classification", Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2017. Get it here. Daya I.B., Chen A.I.H., Shafiee M.J., Wong A., and Yeow J.T.W, "Compensated row-column ultrasound imaging system using three dimensional random fields", Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2017. Get it here. Shafiee M.J., Barshan E., Li F., Chwyl B., Karg M., Scharfenberger C., and Wong A, "Learning Efficient Deep Feature Representations via Transgenerational Genetic Transmission of Environmental Information During E", Proceedings - 2017 IEEE International Conference on Computer Vision Workshops, ICCVW 2017, 2017. Get it here. Chung A.G., Shafiee M.J., and Wong A, "Image restoration via deep-structured stochastically fully-connected conditional random fields (DSFCRFs) for very low-light cond", Proceedings - 2016 13th Conference on Computer and Robot Vision, CRV 2016, 2016. Get it here. Chung A.G., Shafiee M.J., and Wong A, "Random feature maps via a Layered Random Projection (LARP) framework for object classification", Proceedings - International Conference on Image Processing, ICIP, 2016. Get it here. Karimi A.H., Shafiee M.J., Scharfenberger C., Bendaya I., Haider S., Talukdar N., Clausi D.A., and Wong A, "Spatio-temporal saliency detection using abstracted fully-connected graphical models", Proceedings - International Conference on Image Processing, ICIP, 2016. Get it here. Shafiee M.J., Siva P., Fieguth P., and Wong A, "Embedded Motion Detection via Neural Response Mixture Background Modeling", IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops, 2016. Get it here. Shafiee M.J., Siva P., Fieguth P., and Wong A, "Efficient Deep Feature Learning and Extraction via StochasticNets", IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops, 2016. Get it here. Siva P., Shafiee M.J., Jamieson M., and Wong A, "Real-Time, Embedded Scene Invariant Crowd Counting Using Scale-Normalized Histogram of Moving Gradients (HoMG)", IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops, 2016. Get it here. Boroomand A., Li E., Shafiee M.J., Haider M.A., Khalvati F., and Wong A, "A unified Bayesian-based compensated magnetic resonance imaging", Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS, 2016. Get it here. Deglint J., Kazemzadeh F., Shafiee M.J., Li E., Khodadad I., Saini S.S., Wong A., and Clausi D.A, "Virtual spectral multiplexing for applications in in-situ imaging microscopy of transient phenomena", Proceedings of SPIE - The International Society for Optical Engineering, 2015. Get it here. Li F.Y., Shafiee M.J., Chung A.G., Chwyl B., Kazemzadeh F., Wong A., and Zelek J, "High dynamic range map estimation via fully connected random fields with stochastic cliques", Proceedings - International Conference on Image Processing, ICIP, 2015. Get it here. Shafiee M.J., Chung A.G., Wong A., and Fieguth P, "Improved fine structure modeling via guided stochastic clique formation in fully connected conditional random fields", Proceedings - International Conference on Image Processing, ICIP, 2015. Get it here. Haider S.A., Shafiee M.J., Chung A., Khalvati F., Oikonomou A., Wong A., and Haider M.A, "Single-click, semi-automatic lung nodule contouring using hierarchical conditional random fields", Proceedings - International Symposium on Biomedical Imaging, 2015. Get it here. Boroomand A., Shafiee M.J., Wong A., and Bizheva K, "Lateral resolution enhancement via imbricated spectral domain optical coherence tomography in a maximum-a-posterior reconstructi", Progress in Biomedical Optics and Imaging - Proceedings of SPIE, 2015. Get it here. Xu L., Shafiee M.J., Wong A., Li F., Wang L., and Clausi D, "Oil spill candidate detection from SAR imagery using a thresholding-guided stochastic fully-connected conditional random field m", IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops, 2015. Get it here. Li F., Li E., Shafiee M.J., Wong A., and Zelek J, "Dense Depth Map Reconstruction from Sparse Measurements Using a Multilayer Conditional Random Field Model", Proceedings -2015 12th Conference on Computer and Robot Vision, CRV 2015, 2015. Get it here. Siva P., Shafiee M.J., Li F., and Wong A, "PIRM: Fast background subtraction under sudden, local illumination changes via probabilistic illumination range modelling", Proceedings - International Conference on Image Processing, ICIP, 2015. Get it here. Li E., Shafiee M.J., Kazemzadeh F., and Wong A, "Sparse reconstruction of compressed sensing multispectral data using a cross-spectral multilayered conditional random field mode", Proceedings of SPIE - The International Society for Optical Engineering, 2015. Get it here. Kazemzadeh F., Shafiee M.J., Wong A., and Clausi D.A, "Reconstruction of compressive multispectral sensing data using a multilayered conditional random field approach", Proceedings of SPIE - The International Society for Optical Engineering, 2014. Get it here. Shafiee M.J., Wong A., Siva P., and Fieguth P, "Efficient Bayesian inference using fully connected conditional random fields with stochastic cliques", 2014 IEEE International Conference on Image Processing, ICIP 2014, 2015. Get it here. Cameron A., Modhafar A., Khalvati F., Lui D., Shafiee M.J., Wong A., and Haider M, "Multiparametric MRI prostate cancer analysis via a hybrid morphological-textural model", 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2014, 2014. Get it here. Nazemi A., Shafiee M.J., and Azimifar Z, "On road vehicle make and model recognition via sparse feature coding", Iranian Conference on Machine Vision and Image Processing, MVIP, 2015. Get it here. Shafiee M.J., Azimifar Z., Wong A., and Fieguth P, "A novel hierarchical model-based frame rate up-conversion via spatio-temporal conditional random fields", Proceedings - 2011 IEEE InternationalSymposium on Multimedia, ISM 2011, 2015. Get it here. Shafiee M.J., Azimifar Z., and Fieguth P, "Temporal conditional random fields: A conditional state space predictor for visual tracking", 2010 6th Iranian Conference on Machine Vision and Image Processing, MVIP 2010, 2015. Get it here. Shafiee M.J., Azimifar Z., and Fieguth P, "Model-based tracking: Temporal conditional random fields", Proceedings - International Conference on Image Processing, ICIP, 2015. Get it here. Nair S., Abbasi S., Wong A., and Shafiee M.J, "MAPLE-Edge: A Runtime Latency Predictor for Edge Devices", IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops, 2022. Get it here. Xu C., Famouri M., Bathla G., Nair S., Shafiee M.J., and Wong A, "CellDefectNet: A Machine-designed Attention Condenser Network for Electroluminescence-based Photovoltaic Cell Defect Inspection", Proceedings - 2022 19th Conference on Robots and Vision, CRV 2022, 2022. Get it here. Abbasi S., Wong A., and Shafiee M.J, "MAPLE: Microprocessor A Priori for Latency Estimation", IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops, 2022. Get it here. Xu C., Famouri M., Bathla G., Shafiee M.J., and Wong A, "High-Throughput, High-Performance Deep Learning-Driven Light Guide Plate Surface Visual Quality Inspection Tailored for Real-Wor", Proceedings of the 37th AAAI Conference on Artificial Intelligence, AAAI 2023, . Get it here. Shang J.C., Chen Y., Shafiee M.J., and Clausi D.A, "Rink-Agnostic Hockey Rink Registration", MMSports 2023 - Proceedings of the 6th International Workshop on Multimedia Content Analysis in Sports, Co-located with: MM 2023, . Get it here.