Search

Recent applications of deep convolutional neural networks in medical imaging raise concerns about their interpretability. While most explainable deep learning applications use post hoc methods (such as GradCAM) to generate feature attribution maps, there is a new type of case-based reasoning models, namely ProtoPNet and its variants, which identify prototypes during training and compare input image patches with those prototypes. We propose the first medical prototype network (MProtoNet) to extend ProtoPNet to brain tumor classification with 3D multi-parametric magnetic resonance imaging (mpMRI) data. To address different requirements between 2D natural images and 3D mpMRIs especially in terms of localizing attention regions, a new attention module with soft masking and online-CAM loss is introduced. Soft masking helps sharpen attention maps, while online-CAM loss directly utilizes image-level labels when training the attention module. MProtoNet achieves statistically significant improvements in interpretability metrics of both correctness and localization coherence (with a best activation precision of $0.713\pm0.058$) without human-annotated labels during training, when compared with GradCAM and several ProtoPNet variants. The source code is available at https://github.com/aywi/mprotonet., Comment: 15 pages, 5 figures, 1 table; accepted for oral presentation at MIDL 2023 (https://openreview.net/forum?id=6Wbj3QCo4U4 ); camera-ready version

Supplemental material, sj-docx-1-msj-10.1177_13524585231164295 for Employment status, productivity loss, and associated factors among people with multiple sclerosis by Elisabet Rodriguez Llorian, Wei Zhang, Amir Khakban, Kristina Michaux, Scott Patten, Anthony Traboulsee, Jiwon Oh, Shannon Kolind, Alexandre Prat, Roger Tam and Larry D Lynd in Multiple Sclerosis Journal

Influenza and Respiratory Syncytial virus (RSV) infections together contribute significantly to the burden of acute lower respiratory tract infections. Despite the disease burden, no approved RSV vaccine is available. While approved vaccines are available for influenza, seasonal vaccination is required to maintain protection. In addition to both being respiratory viruses, they follow a common seasonality, which warrants the necessity for a concerted vaccination approach. Here, we designed bivalent vaccines by utilizing highly conserved sequences, targeting both influenza A and RSV, as either a chimeric antigen or individual antigens separated by a ribosome skipping sequence. These vaccines were found to be effective in protecting the animals from challenge by either virus, with mechanisms of protection being substantially interrogated in this communication.

Supplemental material, sj-docx-1-msj-10.1177_13524585231164295 for Employment status, productivity loss, and associated factors among people with multiple sclerosis by Elisabet Rodriguez Llorian, Wei Zhang, Amir Khakban, Kristina Michaux, Scott Patten, Anthony Traboulsee, Jiwon Oh, Shannon Kolind, Alexandre Prat, Roger Tam and Larry D Lynd in Multiple Sclerosis Journal

Self-supervised learning (SSL) has been widely applied to learn image representations through exploiting unlabeled images. However, it has not been fully explored in the medical image analysis field. In this work, we propose Saliency-guided Self-Supervised image Transformer (SSiT) for diabetic retinopathy (DR) grading from fundus images. We novelly introduce saliency maps into SSL, with a goal of guiding self-supervised pre-training with domain-specific prior knowledge. Specifically, two saliency-guided learning tasks are employed in SSiT: (1) We conduct saliency-guided contrastive learning based on the momentum contrast, wherein we utilize fundus images' saliency maps to remove trivial patches from the input sequences of the momentum-updated key encoder. And thus, the key encoder is constrained to provide target representations focusing on salient regions, guiding the query encoder to capture salient features. (2) We train the query encoder to predict the saliency segmentation, encouraging preservation of fine-grained information in the learned representations. Extensive experiments are conducted on four publicly-accessible fundus image datasets. The proposed SSiT significantly outperforms other representative state-of-the-art SSL methods on all datasets and under various evaluation settings, establishing the effectiveness of the learned representations from SSiT. The source code is available at https://github.com/YijinHuang/SSiT.

Supplemental material, sj-docx-1-msj-10.1177_13524585211069070 for Productivity loss among people with early multiple sclerosis: A Canadian study by Elisabet Rodriguez Llorian, Wei Zhang, Amir Khakban, Scott Patten, Anthony Traboulsee, Jiwon Oh, Shannon Kolind, Alexandre Prat, Roger Tam and Larry D Lynd in Multiple Sclerosis Journal

Supplemental material, sj-docx-1-msj-10.1177_13524585211069070 for Productivity loss among people with early multiple sclerosis: A Canadian study by Elisabet Rodriguez Llorian, Wei Zhang, Amir Khakban, Scott Patten, Anthony Traboulsee, Jiwon Oh, Shannon Kolind, Alexandre Prat, Roger Tam and Larry D Lynd in Multiple Sclerosis Journal

Supplemental material, sj-pdf-1-msj-10.1177_13524585211023345 for Characterization of multiple sclerosis neuroinflammation and neurodegeneration with relaxation and diffusion basis spectrum imaging by Irene M Vavasour, Peng Sun, Carina Graf, Jackie T Yik, Shannon H Kolind, David KB Li, Roger Tam, Ana-Luiza Sayao, Alice Schabas, Virginia Devonshire, Robert Carruthers, Anthony Traboulsee, GR Wayne Moore, Sheng-Kwei Song and Cornelia Laule in Multiple Sclerosis Journal

Supplemental material, sj-pdf-2-msj-10.1177_13524585211023345 for Characterization of multiple sclerosis neuroinflammation and neurodegeneration with relaxation and diffusion basis spectrum imaging by Irene M Vavasour, Peng Sun, Carina Graf, Jackie T Yik, Shannon H Kolind, David KB Li, Roger Tam, Ana-Luiza Sayao, Alice Schabas, Virginia Devonshire, Robert Carruthers, Anthony Traboulsee, GR Wayne Moore, Sheng-Kwei Song and Cornelia Laule in Multiple Sclerosis Journal

Supplemental material, sj-pdf-5-msj-10.1177_13524585211023345 for Characterization of multiple sclerosis neuroinflammation and neurodegeneration with relaxation and diffusion basis spectrum imaging by Irene M Vavasour, Peng Sun, Carina Graf, Jackie T Yik, Shannon H Kolind, David KB Li, Roger Tam, Ana-Luiza Sayao, Alice Schabas, Virginia Devonshire, Robert Carruthers, Anthony Traboulsee, GR Wayne Moore, Sheng-Kwei Song and Cornelia Laule in Multiple Sclerosis Journal

Supplemental material, sj-pdf-4-msj-10.1177_13524585211023345 for Characterization of multiple sclerosis neuroinflammation and neurodegeneration with relaxation and diffusion basis spectrum imaging by Irene M Vavasour, Peng Sun, Carina Graf, Jackie T Yik, Shannon H Kolind, David KB Li, Roger Tam, Ana-Luiza Sayao, Alice Schabas, Virginia Devonshire, Robert Carruthers, Anthony Traboulsee, GR Wayne Moore, Sheng-Kwei Song and Cornelia Laule in Multiple Sclerosis Journal

Supplemental material, sj-pdf-2-msj-10.1177_13524585211023345 for Characterization of multiple sclerosis neuroinflammation and neurodegeneration with relaxation and diffusion basis spectrum imaging by Irene M Vavasour, Peng Sun, Carina Graf, Jackie T Yik, Shannon H Kolind, David KB Li, Roger Tam, Ana-Luiza Sayao, Alice Schabas, Virginia Devonshire, Robert Carruthers, Anthony Traboulsee, GR Wayne Moore, Sheng-Kwei Song and Cornelia Laule in Multiple Sclerosis Journal

Supplemental material, sj-pdf-3-msj-10.1177_13524585211023345 for Characterization of multiple sclerosis neuroinflammation and neurodegeneration with relaxation and diffusion basis spectrum imaging by Irene M Vavasour, Peng Sun, Carina Graf, Jackie T Yik, Shannon H Kolind, David KB Li, Roger Tam, Ana-Luiza Sayao, Alice Schabas, Virginia Devonshire, Robert Carruthers, Anthony Traboulsee, GR Wayne Moore, Sheng-Kwei Song and Cornelia Laule in Multiple Sclerosis Journal

Supplemental material, sj-pdf-3-msj-10.1177_13524585211023345 for Characterization of multiple sclerosis neuroinflammation and neurodegeneration with relaxation and diffusion basis spectrum imaging by Irene M Vavasour, Peng Sun, Carina Graf, Jackie T Yik, Shannon H Kolind, David KB Li, Roger Tam, Ana-Luiza Sayao, Alice Schabas, Virginia Devonshire, Robert Carruthers, Anthony Traboulsee, GR Wayne Moore, Sheng-Kwei Song and Cornelia Laule in Multiple Sclerosis Journal

Supplemental material, sj-pdf-5-msj-10.1177_13524585211023345 for Characterization of multiple sclerosis neuroinflammation and neurodegeneration with relaxation and diffusion basis spectrum imaging by Irene M Vavasour, Peng Sun, Carina Graf, Jackie T Yik, Shannon H Kolind, David KB Li, Roger Tam, Ana-Luiza Sayao, Alice Schabas, Virginia Devonshire, Robert Carruthers, Anthony Traboulsee, GR Wayne Moore, Sheng-Kwei Song and Cornelia Laule in Multiple Sclerosis Journal

Supplemental material, sj-pdf-4-msj-10.1177_13524585211023345 for Characterization of multiple sclerosis neuroinflammation and neurodegeneration with relaxation and diffusion basis spectrum imaging by Irene M Vavasour, Peng Sun, Carina Graf, Jackie T Yik, Shannon H Kolind, David KB Li, Roger Tam, Ana-Luiza Sayao, Alice Schabas, Virginia Devonshire, Robert Carruthers, Anthony Traboulsee, GR Wayne Moore, Sheng-Kwei Song and Cornelia Laule in Multiple Sclerosis Journal

Additional file 2. SPIRIT 2013 Checklist.

Additional file 1. Sample size justification for sub-cohorts. Description: Sample size justifications for sub-cohorts, prepared by Dr. Maria Pia Sormani.

Additional file 1.

We propose a novel T2 relaxation data analysis method which we have named spectrum analysis for multiple exponentials via experimental condition oriented simulation (SAME-ECOS). SAME-ECOS, which was developed based on a combination of information theory and machine learning neural network algorithms, is tailored for different MR experimental conditions, decomposing multi-exponential decay data into T2 spectra, which had been considered an ill-posed problem using conventional fitting algorithms, including the commonly used non-negative least squares (NNLS) method. Our results demonstrated that, compared with NNLS, the simulation-derived SAME-ECOS model yields much more reliable T2 spectra in a dramatically shorter time, increasing the feasibility of multi-component T2 decay analysis in clinical settings.

Supplemental Material for Advanced imaging findings in progressive solitary sclerosis: a single lesion or a global disease? by Lisa Eunyoung Lee, Jillian K Chan, Emilie Nevill, Adam Soares, Irene M Vavasour, Erin L MacMillan, Hideki Garren, David Clayton, B Mark Keegan, Roger Tam, Anthony L Traboulsee, Shannon H Kolind and Robert L Carruthers in Multiple Sclerosis Journal—Experimental, Translational and Clinical

Supplemental material, MSJ770085_supplementary_appendix for A 24-month advanced magnetic resonance imaging study of multiple sclerosis patients treated with alemtuzumab by Irene M Vavasour, Roger Tam, David KB Li, Cornelia Laule, Carolyn Taylor, Shannon H Kolind, Alex L MacKay, Adil Javed and Anthony Traboulsee in Multiple Sclerosis Journal

Supplemental material, MSO879952 Supplemental Material2 for Magnetic resonance spectroscopy evidence for declining gliosis in MS patients treated with ocrelizumab versus interferon beta-1a by Erin L MacMillan, Julia J Schubert, Irene M Vavasour, Roger Tam, Alexander Rauscher, Carolyn Taylor, Rick White, Hideki Garren, David Clayton, Victoria Levesque, David KB Li, Shannon H Kolind and Anthony L Traboulsee in Multiple Sclerosis Journal – Experimental, Translational and Clinical

Supplemental material, MSO879952 Supplemental Material2 for Magnetic resonance spectroscopy evidence for declining gliosis in MS patients treated with ocrelizumab versus interferon beta-1a by Erin L MacMillan, Julia J Schubert, Irene M Vavasour, Roger Tam, Alexander Rauscher, Carolyn Taylor, Rick White, Hideki Garren, David Clayton, Victoria Levesque, David KB Li, Shannon H Kolind and Anthony L Traboulsee in Multiple Sclerosis Journal – Experimental, Translational and Clinical

Supplemental material, MSO879952 Supplemental Material1 for Magnetic resonance spectroscopy evidence for declining gliosis in MS patients treated with ocrelizumab versus interferon beta-1a by Erin L MacMillan, Julia J Schubert, Irene M Vavasour, Roger Tam, Alexander Rauscher, Carolyn Taylor, Rick White, Hideki Garren, David Clayton, Victoria Levesque, David KB Li, Shannon H Kolind and Anthony L Traboulsee in Multiple Sclerosis Journal – Experimental, Translational and Clinical

Supplemental material, MSO879952 Supplemental Material1 for Magnetic resonance spectroscopy evidence for declining gliosis in MS patients treated with ocrelizumab versus interferon beta-1a by Erin L MacMillan, Julia J Schubert, Irene M Vavasour, Roger Tam, Alexander Rauscher, Carolyn Taylor, Rick White, Hideki Garren, David Clayton, Victoria Levesque, David KB Li, Shannon H Kolind and Anthony L Traboulsee in Multiple Sclerosis Journal – Experimental, Translational and Clinical