Select Publications

Book Chapters

Xie K; Yang Y; Pagnucco M; Song Y, 2022, 'Electron Microscope Image Registration Using Laplacian Sharpening Transformer U-Net', in Lecture Notes in Computer Science, Springer Nature Switzerland, pp. 310 - 319, http://dx.doi.org/10.1007/978-3-031-16446-0_30

Chen Y; Zhang F; Zhang C; Xue T; Zekelman LR; He J; Song Y; Makris N; Rathi Y; Golby AJ; Cai W; O’Donnell LJ, 2022, 'White Matter Tracts are Point Clouds: Neuropsychological Score Prediction and Critical Region Localization via Geometric Deep Learning', in Lecture Notes in Computer Science, Springer Nature Switzerland, pp. 174 - 184, http://dx.doi.org/10.1007/978-3-031-16431-6_17

Wang H; Song Y; Tang Z; Zhang C; Yu J; Liu D; Zhang D; Liu S; Cai W, 2022, 'AI-Enhanced 3D Biomedical Data Analytics for Neuronal Structure Reconstruction', in Humanity Driven AI, Springer International Publishing, pp. 135 - 163, http://dx.doi.org/10.1007/978-3-030-72188-6_7

Wang X; Xiang T; Zhang C; Song Y; Liu D; Huang H; Cai W, 2021, 'BiX-NAS: Searching Efficient Bi-directional Architecture for Medical Image Segmentation', in Medical Image Computing and Computer Assisted Intervention – MICCAI 2021, Springer International Publishing, pp. 229 - 238, http://dx.doi.org/10.1007/978-3-030-87193-2_22

Chen Y; Zhang C; Song Y; Makris N; Rathi Y; Cai W; Zhang F; O’Donnell LJ, 2021, 'Deep Fiber Clustering: Anatomically Informed Unsupervised Deep Learning for Fast and Effective White Matter Parcellation', in Medical Image Computing and Computer Assisted Intervention – MICCAI 2021, Springer International Publishing, pp. 497 - 507, http://dx.doi.org/10.1007/978-3-030-87234-2_47

Hu Y; Meijering E; Xia Y; Song Y, 2021, 'Deformable Convolution and Semi-supervised Learning in Point Clouds for Aneurysm Classification and Segmentation', in Neural Information Processing, Springer International Publishing, pp. 283 - 290, http://dx.doi.org/10.1007/978-3-030-92310-5_33

Guo R; Pagnucco M; Song Y, 2021, 'Learning with Noise: Mask-Guided Attention Model for Weakly Supervised Nuclei Segmentation', in Medical Image Computing and Computer Assisted Intervention – MICCAI 2021, Springer International Publishing, pp. 461 - 470, http://dx.doi.org/10.1007/978-3-030-87196-3_43

Cong C; Liu S; Di Ieva A; Pagnucco M; Berkovsky S; Song Y, 2021, 'Semi-supervised Adversarial Learning for Stain Normalisation in Histopathology Images', in Medical Image Computing and Computer Assisted Intervention – MICCAI 2021, Springer International Publishing, pp. 581 - 591, http://dx.doi.org/10.1007/978-3-030-87237-3_56

Wang H; Zhang C; Yu J; Song Y; Liu S; Chrzanowski W; Cai W, 2021, 'Voxel-Wise Cross-Volume Representation Learning for 3D Neuron Reconstruction', in Machine Learning in Medical Imaging, Springer International Publishing, pp. 248 - 257, http://dx.doi.org/10.1007/978-3-030-87589-3_26

Song Y; Cai W, 2020, 'Visual feature representation in microscopy image classification', in Computer Vision for Microscopy Image Analysis, Elsevier, pp. 73 - 100, http://dx.doi.org/10.1016/B978-0-12-814972-0.00004-7

Cai W; Song Y; Kumar A; Kim J; Feng DD, 2020, 'Content-based large-scale medical image retrieval', in Biomedical Information Technology, Elsevier, pp. 321 - 368, http://dx.doi.org/10.1016/b978-0-12-816034-3.00011-0

Song Y; Cai W, 2017, 'Handling of feature space complexity for texture analysis in medical images', in Biomedical Texture Analysis: Fundamentals, Tools and Challenges, pp. 163 - 191, http://dx.doi.org/10.1016/B978-0-12-812133-7.00006-5

Song Y; Cai W, 2017, 'Chapter 6 Handling of Feature Space Complexity for Texture Analysis in Medical Images', in Biomedical Texture Analysis, Elsevier, pp. 163 - 191, http://dx.doi.org/10.1016/b978-0-12-812133-7.00006-5

Zhang F; Song Y; Cai W; Depeursinge A; Müller H, 2017, 'Text- and Content-Based Medical Image Retrieval in the VISCERAL Retrieval Benchmark', in Cloud-Based Benchmarking of Medical Image Analysis, Springer International Publishing, pp. 237 - 249, http://dx.doi.org/10.1007/978-3-319-49644-3_14

Song Y; Cai W; Eberl S; Fulham MJ; Feng DD, 2014, 'FEATURE-CENTRIC LESION DETECTION AND RETRIEVAL IN THORACIC IMAGES', in Computer Vision in Medical Imaging, WORLD SCIENTIFIC, pp. 75 - 94, http://dx.doi.org/10.1142/9789814460941_0005

Journal articles

Rana P; Sowmya A; Meijering E; Song Y, 2022, 'Data augmentation with improved regularisation and sampling for imbalanced blood cell image classification', Scientific Reports, vol. 12, http://dx.doi.org/10.1038/s41598-022-22882-x

Sandarenu P; Millar EKA; Song Y; Browne L; Beretov J; Lynch J; Graham PH; Jonnagaddala J; Hawkins N; Huang J; Meijering E, 2022, 'Survival prediction in triple negative breast cancer using multiple instance learning of histopathological images', Scientific Reports, vol. 12, pp. 14527, http://dx.doi.org/10.1038/s41598-022-18647-1

Cong C; Liu S; Di Ieva A; Pagnucco M; Berkovsky S; Song Y, 2022, 'Colour adaptive generative networks for stain normalisation of histopathology images', Medical Image Analysis, vol. 82, pp. 102580, http://dx.doi.org/10.1016/j.media.2022.102580

Jiang J; Wang D; Song Y; Sachdev PS; Wen W, 2022, 'Computer-aided extraction of select MRI markers of cerebral small vessel disease: A systematic review', NeuroImage, vol. 261, pp. 119528, http://dx.doi.org/10.1016/j.neuroimage.2022.119528

Xiang T; Song Y; Zhang C; Liu D; Chen M; Zhang F; Huang H; O'Donnell L; Cai W, 2022, 'DSNet: A Dual-Stream Framework for Weakly-Supervised Gigapixel Pathology Image Analysis', IEEE Transactions on Medical Imaging, vol. 41, pp. 2180 - 2190, http://dx.doi.org/10.1109/TMI.2022.3157983

Ma Y; Zhang C; Cabezas M; Song Y; Tang Z; Liu D; Cai W; Barnett M; Wang C, 2022, 'Multiple Sclerosis Lesion Analysis in Brain Magnetic Resonance Images: Techniques and Clinical Applications', IEEE Journal of Biomedical and Health Informatics, vol. 26, pp. 2680 - 2692, http://dx.doi.org/10.1109/JBHI.2022.3151741

Xiang T; Zhang C; Wang X; Song Y; Liu D; Huang H; Cai W, 2022, 'Towards bi-directional skip connections in encoder-decoder architectures and beyond', Medical Image Analysis, vol. 78, http://dx.doi.org/10.1016/j.media.2022.102420

Liu D; Zhang C; Song Y; Huang H; Wang C; Barnett M; Cai W, 2022, 'Decompose to Adapt: Cross-domain Object Detection via Feature Disentanglement', IEEE Transactions on Multimedia, http://dx.doi.org/10.1109/TMM.2022.3141614

Zhu J; Bolsterlee B; Chow BVY; Cai C; Herbert RD; Song Y; Meijering E, 2021, 'Deep learning methods for automatic segmentation of lower leg muscles and bones from MRI scans of children with and without cerebral palsy', NMR in Biomedicine, vol. 34, pp. e4609, http://dx.doi.org/10.1002/nbm.4609

Rana P; Sowmya A; Meijering E; Song Y, 2021, 'Estimation of three-dimensional chromatin morphology for nuclear classification and characterisation', Scientific Reports, vol. 11, http://dx.doi.org/10.1038/s41598-021-82985-9

Liu D; Zhang D; Song Y; Huang H; Cai W, 2021, 'Panoptic Feature Fusion Net: A Novel Instance Segmentation Paradigm for Biomedical and Biological Images', IEEE Transactions on Image Processing, vol. 30, pp. 2045 - 2059, http://dx.doi.org/10.1109/TIP.2021.3050668

Liu D; Zhang D; Song Y; Zhang F; O'Donnell L; Huang H; Chen M; Cai W, 2021, 'PDAM: A Panoptic-Level Feature Alignment Framework for Unsupervised Domain Adaptive Instance Segmentation in Microscopy Images', IEEE Transactions on Medical Imaging, vol. 40, pp. 154 - 165, http://dx.doi.org/10.1109/TMI.2020.3023466

Wu Y; Xia Y; Song Y; Zhang Y; Cai W, 2020, 'NFN+: A novel network followed network for retinal vessel segmentation', Neural Networks, vol. 126, pp. 153 - 162, http://dx.doi.org/10.1016/j.neunet.2020.02.018

Jia H; Xia Y; Song Y; Zhang D; Huang H; Zhang Y; Cai W, 2020, '3D APA-Net: 3D Adversarial Pyramid Anisotropic Convolutional Network for Prostate Segmentation in MR Images', IEEE Transactions on Medical Imaging, vol. 39, pp. 447 - 457, http://dx.doi.org/10.1109/TMI.2019.2928056

Zheng Y; Meng F; Liu J; Guo B; Song Y; Zhang X; Wang L, 2020, 'Fourier Transform to Group Feature on Generated Coarser Contours for Fast 2D Shape Matching', IEEE Access, vol. 8, pp. 90141 - 90152, http://dx.doi.org/10.1109/ACCESS.2020.2994234

Rana P; Sowmya A; Meijering E; Song Y, 2020, 'Estimation of Three-Dimensional Chromatin Morphology for Nuclear Classification and Characterisation', , http://dx.doi.org/10.1101/2020.07.29.226498

Khanal D; Zhang F; Song Y; Hau H; Gautam A; Yamaguchi S; Uertz J; Mills S; Kondyurin A; Knowles JC; Georgiou G; Ramzan I; Cai W; Ng KW; Chrzanowski W, 2019, 'Biological impact of nanodiamond particles–label free, high-resolution methods for nanotoxicity assessment', Nanotoxicology, vol. 13, pp. 1210 - 1226, http://dx.doi.org/10.1080/17435390.2019.1650970

Xie Y; Xia Y; Zhang J; Song Y; Feng D; Fulham M; Cai W, 2019, 'Knowledge-based Collaborative Deep Learning for Benign-Malignant Lung Nodule Classification on Chest CT', IEEE Transactions on Medical Imaging, vol. 38, pp. 991 - 1004, http://dx.doi.org/10.1109/TMI.2018.2876510

Gao C; He X; Gan D; Chen X; Feng F; Li Y; Chua T; Yao L; Song Y; Jin D, 2019, 'Learning to Recommend with Multiple Cascading Behaviors', IEEE Transactions on Knowledge and Data Engineering, pp. 1 - 1, http://dx.doi.org/10.1109/TKDE.2019.2958808

Liu S; Zhang D; Song Y; Peng H; Cai W, 2018, 'Automated 3-D Neuron Tracing with Precise Branch Erasing and Confidence Controlled Back Tracking', IEEE Transactions on Medical Imaging, vol. 37, pp. 2441 - 2452, http://dx.doi.org/10.1109/TMI.2018.2833420

Pan Y; Xia Y; Song Y; Cai W, 2018, 'Locality constrained encoding of frequency and spatial information for image classification', Multimedia Tools and Applications, vol. 77, pp. 24891 - 24907, http://dx.doi.org/10.1007/s11042-018-5712-3

Tareef A; Song Y; Huang H; Feng D; Chen M; Wang Y; Cai W, 2018, 'Multi-Pass Fast Watershed for Accurate Segmentation of Overlapping Cervical Cells', IEEE Transactions on Medical Imaging, vol. 37, pp. 2044 - 2059, http://dx.doi.org/10.1109/TMI.2018.2815013

Meng F; Shan D; Shi R; Song Y; Guo B; Cai W, 2018, 'Merged region based image retrieval', Journal of Visual Communication and Image Representation, vol. 55, pp. 572 - 585, http://dx.doi.org/10.1016/j.jvcir.2018.07.003

Zhang F; Savadjiev P; Cai W; Song Y; Rathi Y; Tunç B; Parker D; Kapur T; Schultz RT; Makris N; Verma R; O'Donnell LJ, 2018, 'Whole brain white matter connectivity analysis using machine learning: An application to autism', NeuroImage, vol. 172, pp. 826 - 837, http://dx.doi.org/10.1016/j.neuroimage.2017.10.029

Zhang F; Wu W; Ning L; McAnulty G; Waber D; Gagoski B; Sarill K; Hamoda HM; Song Y; Cai W; Rathi Y; O'Donnell LJ, 2018, 'Suprathreshold fiber cluster statistics: Leveraging white matter geometry to enhance tractography statistical analysis', NeuroImage, vol. 171, pp. 341 - 354, http://dx.doi.org/10.1016/j.neuroimage.2018.01.006

Zhang D; Liu S; Song Y; Feng D; Peng H; Cai W, 2018, 'Automated 3D Soma Segmentation with Morphological Surface Evolution for Neuron Reconstruction', Neuroinformatics, vol. 16, pp. 153 - 166, http://dx.doi.org/10.1007/s12021-017-9353-x

Jia H; Xia Y; Song Y; Cai W; Fulham M; Feng DD, 2018, 'Atlas registration and ensemble deep convolutional neural network-based prostate segmentation using magnetic resonance imaging', Neurocomputing, vol. 275, pp. 1358 - 1369, http://dx.doi.org/10.1016/j.neucom.2017.09.084

Meng F; Shi R; Shan D; Song Y; He W; Cai W, 2017, 'Multi-sensor image fusion based on regional characteristics', International Journal of Distributed Sensor Networks, vol. 13, http://dx.doi.org/10.1177/1550147717741105

Song Y; Li Q; Huang H; Feng D; Chen M; Cai W, 2017, 'Low Dimensional Representation of Fisher Vectors for Microscopy Image Classification', IEEE Transactions on Medical Imaging, vol. 36, pp. 1636 - 1649, http://dx.doi.org/10.1109/TMI.2017.2687466

Tareef A; Song Y; Huang H; Wang Y; Feng D; Chen M; Cai W, 2017, 'Optimizing the cervix cytological examination based on deep learning and dynamic shape modeling', Neurocomputing, vol. 248, pp. 28 - 40, http://dx.doi.org/10.1016/j.neucom.2017.01.093

Song Y; Li Q; Zhang F; Huang H; Feng D; Wang Y; Chen M; Cai W, 2017, 'Dual discriminative local coding for tissue aging analysis', Medical Image Analysis, vol. 38, pp. 65 - 76, http://dx.doi.org/10.1016/j.media.2016.10.001

Tareef A; Song Y; Cai W; Huang H; Chang H; Wang Y; Fulham M; Feng D; Chen M, 2017, 'Automatic segmentation of overlapping cervical smear cells based on local distinctive features and guided shape deformation', Neurocomputing, vol. 221, pp. 94 - 107, http://dx.doi.org/10.1016/j.neucom.2016.09.070

Song Y; Li Q; Feng D; Zou JJ; Cai W, 2016, 'Texture image classification with discriminative neural networks', Computational Visual Media, vol. 2, pp. 367 - 377, http://dx.doi.org/10.1007/s41095-016-0060-6

Yang MY; Verschuer J; Shi Y; Song Y; Katsifis A; Eberl S; Wong K; Brannan JD; Cai W; Finlay WH; Chan HK, 2016, 'The effect of device resistance and inhalation flow rate on the lung deposition of orally inhaled mannitol dry powder', International Journal of Pharmaceutics, vol. 513, pp. 294 - 301, http://dx.doi.org/10.1016/j.ijpharm.2016.09.047

Song Y; Cai W; Huang H; Feng D; Wang Y; Chen M, 2016, 'Bioimage classification with subcategory discriminant transform of high dimensional visual descriptors', BMC Bioinformatics, vol. 17, http://dx.doi.org/10.1186/s12859-016-1318-9


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