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1,319 results on '"Wells, William M."'

1. Calibrating Expressions of Certainty

Author

Wang, Peiqi, Lam, Barbara D., Liu, Yingcheng, Asgari-Targhi, Ameneh, Panda, Rameswar, Wells, William M., Kapur, Tina, and Golland, Polina

Subjects
Computer Science - Computation and Language, Computer Science - Machine Learning
Abstract

We present a novel approach to calibrating linguistic expressions of certainty, e.g., "Maybe" and "Likely". Unlike prior work that assigns a single score to each certainty phrase, we model uncertainty as distributions over the simplex to capture their semantics more accurately. To accommodate this new representation of certainty, we generalize existing measures of miscalibration and introduce a novel post-hoc calibration method. Leveraging these tools, we analyze the calibration of both humans (e.g., radiologists) and computational models (e.g., language models) and provide interpretable suggestions to improve their calibration.

Published
2024

2. Intraoperative Registration by Cross-Modal Inverse Neural Rendering

Author

Fehrentz, Maximilian, Azampour, Mohammad Farid, Dorent, Reuben, Rasheed, Hassan, Galvin, Colin, Golby, Alexandra, Wells, William M., Frisken, Sarah, Navab, Nassir, and Haouchine, Nazim

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

We present in this paper a novel approach for 3D/2D intraoperative registration during neurosurgery via cross-modal inverse neural rendering. Our approach separates implicit neural representation into two components, handling anatomical structure preoperatively and appearance intraoperatively. This disentanglement is achieved by controlling a Neural Radiance Field's appearance with a multi-style hypernetwork. Once trained, the implicit neural representation serves as a differentiable rendering engine, which can be used to estimate the surgical camera pose by minimizing the dissimilarity between its rendered images and the target intraoperative image. We tested our method on retrospective patients' data from clinical cases, showing that our method outperforms state-of-the-art while meeting current clinical standards for registration. Code and additional resources can be found at https://maxfehrentz.github.io/style-ngp/., Comment: Accepted at MICCAI 2024

Published
2024

3. Learning to Match 2D Keypoints Across Preoperative MR and Intraoperative Ultrasound

Author

Rasheed, Hassan, Dorent, Reuben, Fehrentz, Maximilian, Kapur, Tina, Wells, William M., III, Golby, Alexandra, Frisken, Sarah, Schnabel, Julia A., Haouchine, Nazim, Goos, Gerhard, Series Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Gomez, Alberto, editor, Khanal, Bishesh, editor, King, Andrew, editor, and Namburete, Ana, editor

Published
2025
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4. Unified Brain MR-Ultrasound Synthesis using Multi-Modal Hierarchical Representations

Author

Dorent, Reuben, Haouchine, Nazim, Kögl, Fryderyk, Joutard, Samuel, Juvekar, Parikshit, Torio, Erickson, Golby, Alexandra, Ourselin, Sebastien, Frisken, Sarah, Vercauteren, Tom, Kapur, Tina, and Wells, William M.

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

We introduce MHVAE, a deep hierarchical variational auto-encoder (VAE) that synthesizes missing images from various modalities. Extending multi-modal VAEs with a hierarchical latent structure, we introduce a probabilistic formulation for fusing multi-modal images in a common latent representation while having the flexibility to handle incomplete image sets as input. Moreover, adversarial learning is employed to generate sharper images. Extensive experiments are performed on the challenging problem of joint intra-operative ultrasound (iUS) and Magnetic Resonance (MR) synthesis. Our model outperformed multi-modal VAEs, conditional GANs, and the current state-of-the-art unified method (ResViT) for synthesizing missing images, demonstrating the advantage of using a hierarchical latent representation and a principled probabilistic fusion operation. Our code is publicly available \url{https://github.com/ReubenDo/MHVAE}., Comment: Accepted at MICCAI 2023

Published
2023
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5. ReMIND: The Brain Resection Multimodal Imaging Database

Author

Juvekar, Parikshit, Dorent, Reuben, Kögl, Fryderyk, Torio, Erickson, Barr, Colton, Rigolo, Laura, Galvin, Colin, Jowkar, Nick, Kazi, Anees, Haouchine, Nazim, Cheema, Harneet, Navab, Nassir, Pieper, Steve, Wells, William M., Bi, Wenya Linda, Golby, Alexandra, Frisken, Sarah, and Kapur, Tina

Published
2024
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6. Sample-Specific Debiasing for Better Image-Text Models

Author

Wang, Peiqi, Liu, Yingcheng, Ko, Ching-Yun, Wells, William M., Berkowitz, Seth, Horng, Steven, and Golland, Polina

Subjects
Computer Science - Machine Learning, Computer Science - Computer Vision and Pattern Recognition
Abstract

Self-supervised representation learning on image-text data facilitates crucial medical applications, such as image classification, visual grounding, and cross-modal retrieval. One common approach involves contrasting semantically similar (positive) and dissimilar (negative) pairs of data points. Drawing negative samples uniformly from the training data set introduces false negatives, i.e., samples that are treated as dissimilar but belong to the same class. In healthcare data, the underlying class distribution is nonuniform, implying that false negatives occur at a highly variable rate. To improve the quality of learned representations, we develop a novel approach that corrects for false negatives. Our method can be viewed as a variant of debiased contrastive learning that uses estimated sample-specific class probabilities. We provide theoretical analysis of the objective function and demonstrate the proposed approach on both image and paired image-text data sets. Our experiments illustrate empirical advantages of sample-specific debiasing., Comment: Machine Learning for Healthcare Conference 2023

Published
2023

7. Deep Learning for Detection and Localization of B-Lines in Lung Ultrasound

Author

Lucassen, Ruben T., Jafari, Mohammad H., Duggan, Nicole M., Jowkar, Nick, Mehrtash, Alireza, Fischetti, Chanel, Bernier, Denie, Prentice, Kira, Duhaime, Erik P., Jin, Mike, Abolmaesumi, Purang, Heslinga, Friso G., Veta, Mitko, Duran-Mendicuti, Maria A., Frisken, Sarah, Shyn, Paul B., Golby, Alexandra J., Boyer, Edward, Wells, William M., Goldsmith, Andrew J., and Kapur, Tina

Subjects
Electrical Engineering and Systems Science - Image and Video Processing
Abstract

Lung ultrasound (LUS) is an important imaging modality used by emergency physicians to assess pulmonary congestion at the patient bedside. B-line artifacts in LUS videos are key findings associated with pulmonary congestion. Not only can the interpretation of LUS be challenging for novice operators, but visual quantification of B-lines remains subject to observer variability. In this work, we investigate the strengths and weaknesses of multiple deep learning approaches for automated B-line detection and localization in LUS videos. We curate and publish, BEDLUS, a new ultrasound dataset comprising 1,419 videos from 113 patients with a total of 15,755 expert-annotated B-lines. Based on this dataset, we present a benchmark of established deep learning methods applied to the task of B-line detection. To pave the way for interpretable quantification of B-lines, we propose a novel "single-point" approach to B-line localization using only the point of origin. Our results show that (a) the area under the receiver operating characteristic curve ranges from 0.864 to 0.955 for the benchmarked detection methods, (b) within this range, the best performance is achieved by models that leverage multiple successive frames as input, and (c) the proposed single-point approach for B-line localization reaches an F1-score of 0.65, performing on par with the inter-observer agreement. The dataset and developed methods can facilitate further biomedical research on automated interpretation of lung ultrasound with the potential to expand the clinical utility., Comment: 10 pages, 4 figures

Published
2023

8. Using Multiple Instance Learning to Build Multimodal Representations

Author

Wang, Peiqi, Wells, William M., Berkowitz, Seth, Horng, Steven, and Golland, Polina

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Image-text multimodal representation learning aligns data across modalities and enables important medical applications, e.g., image classification, visual grounding, and cross-modal retrieval. In this work, we establish a connection between multimodal representation learning and multiple instance learning. Based on this connection, we propose a generic framework for constructing permutation-invariant score functions with many existing multimodal representation learning approaches as special cases. Furthermore, we use the framework to derive a novel contrastive learning approach and demonstrate that our method achieves state-of-the-art results in several downstream tasks.

Published
2022
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9. Patient-Specific Real-Time Segmentation in Trackerless Brain Ultrasound

Author

Dorent, Reuben, Torio, Erickson, Haouchine, Nazim, Galvin, Colin, Frisken, Sarah, Golby, Alexandra, Kapur, Tina, Wells, William M., Goos, Gerhard, Series Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Linguraru, Marius George, editor, Dou, Qi, editor, Feragen, Aasa, editor, Giannarou, Stamatia, editor, Glocker, Ben, editor, Lekadir, Karim, editor, and Schnabel, Julia A., editor

Published
2024
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10. TractoSCR: A Novel Supervised Contrastive Regression Framework for Prediction of Neurocognitive Measures Using Multi-Site Harmonized Diffusion MRI Tractography

Author

Xue, Tengfei, Zhang, Fan, Zekelman, Leo R., Zhang, Chaoyi, Chen, Yuqian, Cetin-Karayumak, Suheyla, Pieper, Steve, Wells, William M., Rathi, Yogesh, Makris, Nikos, Cai, Weidong, and O'Donnell, Lauren J.

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Neuroimaging-based prediction of neurocognitive measures is valuable for studying how the brain's structure relates to cognitive function. However, the accuracy of prediction using popular linear regression models is relatively low. We propose a novel deep regression method, namely TractoSCR, that allows full supervision for contrastive learning in regression tasks using diffusion MRI tractography. TractoSCR performs supervised contrastive learning by using the absolute difference between continuous regression labels (i.e. neurocognitive scores) to determine positive and negative pairs. We apply TractoSCR to analyze a large-scale dataset including multi-site harmonized diffusion MRI and neurocognitive data from 8735 participants in the Adolescent Brain Cognitive Development (ABCD) Study. We extract white matter microstructural measures using a fine parcellation of white matter tractography into fiber clusters. Using these measures, we predict three scores related to domains of higher-order cognition (general cognitive ability, executive function, and learning/memory). To identify important fiber clusters for prediction of these neurocognitive scores, we propose a permutation feature importance method for high-dimensional data. We find that TractoSCR improves the accuracy of neurocognitive score prediction compared to other state-of-the-art methods. We find that the most predictive fiber clusters are predominantly located within the superficial white matter and projection tracts, particularly the superficial frontal white matter and striato-frontal connections. Overall, our results demonstrate the utility of contrastive representation learning methods for regression, and in particular for improving neuroimaging-based prediction of higher-order cognitive abilities., Comment: 28 pages, 4 figures

Published
2022

11. SuperWarp: Supervised Learning and Warping on U-Net for Invariant Subvoxel-Precise Registration

Author

Young, Sean I., Balbastre, Yaël, Dalca, Adrian V., Wells, William M., Iglesias, Juan Eugenio, and Fischl, Bruce

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Electrical Engineering and Systems Science - Image and Video Processing
Abstract

In recent years, learning-based image registration methods have gradually moved away from direct supervision with target warps to instead use self-supervision, with excellent results in several registration benchmarks. These approaches utilize a loss function that penalizes the intensity differences between the fixed and moving images, along with a suitable regularizer on the deformation. In this paper, we argue that the relative failure of supervised registration approaches can in part be blamed on the use of regular U-Nets, which are jointly tasked with feature extraction, feature matching, and estimation of deformation. We introduce one simple but crucial modification to the U-Net that disentangles feature extraction and matching from deformation prediction, allowing the U-Net to warp the features, across levels, as the deformation field is evolved. With this modification, direct supervision using target warps begins to outperform self-supervision approaches that require segmentations, presenting new directions for registration when images do not have segmentations. We hope that our findings in this preliminary workshop paper will re-ignite research interest in supervised image registration techniques. Our code is publicly available from https://github.com/balbasty/superwarp.

Published
2022

12. Equivariant Filters for Efficient Tracking in 3D Imaging

Author

Moyer, Daniel, Turk, Esra Abaci, Grant, P Ellen, Wells, William M., and Golland, Polina

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Quantitative Biology - Quantitative Methods
Abstract

We demonstrate an object tracking method for 3D images with fixed computational cost and state-of-the-art performance. Previous methods predicted transformation parameters from convolutional layers. We instead propose an architecture that does not include either flattening of convolutional features or fully connected layers, but instead relies on equivariant filters to preserve transformations between inputs and outputs (e.g. rot./trans. of inputs rotate/translate outputs). The transformation is then derived in closed form from the outputs of the filters. This method is useful for applications requiring low latency, such as real-time tracking. We demonstrate our model on synthetically augmented adult brain MRI, as well as fetal brain MRI, which is the intended use-case., Comment: MICCAI 2021 Early Accept

Published
2021

13. Multimodal Representation Learning via Maximization of Local Mutual Information

Author

Liao, Ruizhi, Moyer, Daniel, Cha, Miriam, Quigley, Keegan, Berkowitz, Seth, Horng, Steven, Golland, Polina, and Wells, William M.

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition
Abstract

We propose and demonstrate a representation learning approach by maximizing the mutual information between local features of images and text. The goal of this approach is to learn useful image representations by taking advantage of the rich information contained in the free text that describes the findings in the image. Our method trains image and text encoders by encouraging the resulting representations to exhibit high local mutual information. We make use of recent advances in mutual information estimation with neural network discriminators. We argue that the sum of local mutual information is typically a lower bound on the global mutual information. Our experimental results in the downstream image classification tasks demonstrate the advantages of using local features for image-text representation learning., Comment: In Proceedings of International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2021

Published
2021
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14. Learning Expected Appearances for Intraoperative Registration During Neurosurgery

Author

Haouchine, Nazim, Dorent, Reuben, Juvekar, Parikshit, Torio, Erickson, Wells, William M., III, Kapur, Tina, Golby, Alexandra J., Frisken, Sarah, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Greenspan, Hayit, editor, Madabhushi, Anant, editor, Mousavi, Parvin, editor, Salcudean, Septimiu, editor, Duncan, James, editor, Syeda-Mahmood, Tanveer, editor, and Taylor, Russell, editor

Published
2023
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15. MetaMorph: Learning Metamorphic Image Transformation with Appearance Changes

Author

Wang, Jian, Xing, Jiarui, Druzgal, Jason, Wells, William M., III, Zhang, Miaomiao, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Frangi, Alejandro, editor, de Bruijne, Marleen, editor, Wassermann, Demian, editor, and Navab, Nassir, editor

Published
2023
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16. Using Multiple Instance Learning to Build Multimodal Representations

Author

Wang, Peiqi, Wells, William M., Berkowitz, Seth, Horng, Steven, Golland, Polina, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Frangi, Alejandro, editor, de Bruijne, Marleen, editor, Wassermann, Demian, editor, and Navab, Nassir, editor

Published
2023
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17. DEMI: Discriminative Estimator of Mutual Information

Author

Liao, Ruizhi, Moyer, Daniel, Golland, Polina, and Wells, William M.

Subjects
Computer Science - Machine Learning, Statistics - Machine Learning
Abstract

Estimating mutual information between continuous random variables is often intractable and extremely challenging for high-dimensional data. Recent progress has leveraged neural networks to optimize variational lower bounds on mutual information. Although showing promise for this difficult problem, the variational methods have been theoretically and empirically proven to have serious statistical limitations: 1) many methods struggle to produce accurate estimates when the underlying mutual information is either low or high; 2) the resulting estimators may suffer from high variance. Our approach is based on training a classifier that provides the probability that a data sample pair is drawn from the joint distribution rather than from the product of its marginal distributions. Moreover, we establish a direct connection between mutual information and the average log odds estimate produced by the classifier on a test set, leading to a simple and accurate estimator of mutual information. We show theoretically that our method and other variational approaches are equivalent when they achieve their optimum, while our method sidesteps the variational bound. Empirical results demonstrate high accuracy of our approach and the advantages of our estimator in the context of representation learning. Our demo is available at https://github.com/RayRuizhiLiao/demi_mi_estimator.

Published
2020

19. On the Dataset Quality Control for Image Registration Evaluation

Author

Luo, Jie, Ma, Guangshen, Haouchine, Nazim, Xu, Zhe, Wang, Yixin, Kapur, Tina, Ning, Lipeng, Wells, William M., III, Frisken, Sarah, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Wang, Linwei, editor, Dou, Qi, editor, Fletcher, P. Thomas, editor, Speidel, Stefanie, editor, and Li, Shuo, editor

Published
2022
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20. Double-Uncertainty Guided Spatial and Temporal Consistency Regularization Weighting for Learning-Based Abdominal Registration

Author

Xu, Zhe, Luo, Jie, Lu, Donghuan, Yan, Jiangpeng, Frisken, Sarah, Jagadeesan, Jayender, Wells, William M., III, Li, Xiu, Zheng, Yefeng, Tong, Raymond Kai-yu, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Wang, Linwei, editor, Dou, Qi, editor, Fletcher, P. Thomas, editor, Speidel, Stefanie, editor, and Li, Shuo, editor

Published
2022
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21. Probabilistic Image Registration via Deep Multi-class Classification: Characterizing Uncertainty

Author

Sedghi, Alireza, Kapur, Tina, Luo, Jie, Mousavi, Parvin, Wells, William M., III, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Greenspan, Hayit, editor, Tanno, Ryutaro, editor, Erdt, Marius, editor, Arbel, Tal, editor, Baumgartner, Christian, editor, Dalca, Adrian, editor, Sudre, Carole H., editor, Wells, William M., editor, Drechsler, Klaus, editor, Linguraru, Marius George, editor, Oyarzun Laura, Cristina, editor, Shekhar, Raj, editor, Wesarg, Stefan, editor, and González Ballester, Miguel Ángel, editor

Published
2019
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22. Registration of longitudinal spine CTs for monitoring lesion growth

Author

Sanhinova, Malika, primary, Haouchine, Nazim, additional, Pieper, Steve, additional, Wells, William M., additional, Balboni, Tracy A., additional, Spektor, Alexander, additional, Huynh, Mai Anh, additional, Guenette, Jeffrey P., additional, Czajkowski, Bryan, additional, Caplan, Sarah, additional, Doyle, Patrick, additional, Kang, Heejoo, additional, Hackney, David B., additional, and Alkalay, Ron N., additional

Published
2024
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24. TractoSCR: a novel supervised contrastive regression framework for prediction of neurocognitive measures using multi-site harmonized diffusion MRI tractography.

Author

Tengfei Xue, Fan Zhang, Zekelman, Leo R., Chaoyi Zhang, Yuqian Chen, Cetin-Karayumak, Suheyla, Pieper, Steve, Wells, William M., Rathi, Yogesh, Makris, Nikos, Weidong Cai, and O'Donnell, Lauren J.

Subjects
DIFFUSION tensor imaging, DIFFUSION magnetic resonance imaging, COGNITIVE ability, WHITE matter (Nerve tissue), NEURAL development
Abstract

Neuroimaging-based prediction of neurocognitive measures is valuable for studying how the brain's structure relates to cognitive function. However, the accuracy of prediction using popular linear regression models is relatively low. We propose a novel deep regression method, namely TractoSCR, that allows full supervision for contrastive learning in regression tasks using diffusion MRI tractography. TractoSCR performs supervised contrastive learning by using the absolute difference between continuous regression labels (i.e., neurocognitive scores) to determine positive and negative pairs. We apply TractoSCR to analyze a large-scale dataset including multi-site harmonized diffusion MRI and neurocognitive data from 8,735 participants in the Adolescent Brain Cognitive Development (ABCD) Study. We extract white matter microstructural measures using a fine parcellation of white matter tractography into fiber clusters. Using these measures, we predict three scores related to domains of higher-order cognition (general cognitive ability, executive function, and learning/memory). To identify important fiber clusters for prediction of these neurocognitive scores, we propose a permutation feature importance method for high-dimensional data. We find that TractoSCR obtains significantly higher accuracy of neurocognitive score prediction compared to other state-of-the-art methods. We find that the most predictive fiber clusters are predominantly located within the superficial white matter and projection tracts, particularly the superficial frontal white matter and striato-frontal connections. Overall, our results demonstrate the utility of contrastive representation learning methods for regression, and in particular for improving neuroimaging-based prediction of higher-order cognitive abilities. [ABSTRACT FROM AUTHOR]

Published
2024
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25. On the Applicability of Registration Uncertainty

Author

Luo, Jie, Sedghi, Alireza, Popuri, Karteek, Cobzas, Dana, Zhang, Miaomiao, Preiswerk, Frank, Toews, Matthew, Golby, Alexandra, Sugiyama, Masashi, Wells, William M., III, Frisken, Sarah, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Shen, Dinggang, editor, Liu, Tianming, editor, Peters, Terry M., editor, Staib, Lawrence H., editor, Essert, Caroline, editor, Zhou, Sean, editor, Yap, Pew-Thian, editor, and Khan, Ali, editor

Published
2019
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29. Efficient Laplace Approximation for Bayesian Registration Uncertainty Quantification

Author

Wang, Jian, Wells, William M., III, Golland, Polina, Zhang, Miaomiao, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Weikum, Gerhard, Series Editor, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Frangi, Alejandro F., editor, Schnabel, Julia A., editor, Davatzikos, Christos, editor, Alberola-López, Carlos, editor, and Fichtinger, Gabor, editor

Published
2018
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33. ReMIND: The Brain Resection Multimodal Imaging Database

Author

Juvekar, Parikshit, primary, Dorent, Reuben, additional, Kogl, Fryderyk, additional, Torio, Erickson, additional, Barr, Colton, additional, Rigolo, Laura, additional, Galvin, Colin, additional, Jowkar, Nick, additional, Kazi, Anees, additional, Haouchine, Nazim, additional, Cheema, Harneet, additional, Navab, Nassir, additional, Pieper, Steve, additional, Wells, William M., additional, Bi, Wenya L, additional, Golby, Alexandra, additional, Frisken, Sarah, additional, and Kapur, Tina, additional

Published
2023
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35. Contributors

Author

Bauer, Martin, primary, Chakraborty, Rudrasis, additional, Charlier, Benjamin, additional, Charon, Nicolas, additional, Choi, Hyo-young, additional, Damon, James, additional, Devilliers, Loic, additional, Feragen, Aasa, additional, Fletcher, Tom, additional, Glaunès, Joan, additional, Golland, Polina, additional, Gori, Pietro, additional, Hong, Junpyo, additional, Joshi, Sarang, additional, Jung, Sungkyu, additional, Liu, Zhiyuan, additional, Lorenzi, Marco, additional, Marron, J.S., additional, Marsland, Stephen, additional, Miolane, Nina, additional, Modersitzki, Jan, additional, Modin, Klas, additional, Niethammer, Marc, additional, Nye, Tom, additional, Paniagua, Beatriz, additional, Pennec, Xavier, additional, Pizer, Stephen M., additional, Polzin, Thomas, additional, Risser, Laurent, additional, Roussillon, Pierre, additional, Schulz, Jörn, additional, Sharma, Ankur, additional, Sommer, Stefan, additional, Srivastava, Anuj, additional, Tu, Liyun, additional, Vemuri, Baba C., additional, Vialard, François-Xavier, additional, Vicory, Jared, additional, Wang, Jiyao, additional, Wells, William M., additional, Zhang, Miaomiao, additional, and Zhang, Ruiyi, additional

Published
2020
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36. Transfer Learning for Domain Adaptation in MRI: Application in Brain Lesion Segmentation

Author

Ghafoorian, Mohsen, Mehrtash, Alireza, Kapur, Tina, Karssemeijer, Nico, Marchiori, Elena, Pesteie, Mehran, Guttmann, Charles R. G., de Leeuw, Frank-Erik, Tempany, Clare M., van Ginneken, Bram, Fedorov, Andriy, Abolmaesumi, Purang, Platel, Bram, Wells, William M., III, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Weikum, Gerhard, Series Editor, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Descoteaux, Maxime, editor, Maier-Hein, Lena, editor, Franz, Alfred, editor, Jannin, Pierre, editor, Collins, D. Louis, editor, and Duchesne, Simon, editor

Published
2017
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37. Inferring Disease Status by Non-parametric Probabilistic Embedding

Author

Batmanghelich, Nematollah Kayhan, Saeedi, Ardavan, Estepar, Raul San Jose, Cho, Michael, Wells, William M., III, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Müller, Henning, editor, Kelm, B. Michael, editor, Arbel, Tal, editor, Cai, Weidong, editor, Cardoso, M. Jorge, editor, Langs, Georg, editor, Menze, Bjoern, editor, Metaxas, Dimitris, editor, Montillo, Albert, editor, Wells III, William M., editor, Zhang, Shaoting, editor, Chung, Albert C.S., editor, Jenkinson, Mark, editor, and Ribbens, Annemie, editor

Published
2017
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38. A Likelihood-Free Approach for Characterizing Heterogeneous Diseases in Large-Scale Studies

Author

Schabdach, Jenna, Wells, William M., III, Cho, Michael, Batmanghelich, Kayhan N., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Niethammer, Marc, editor, Styner, Martin, editor, Aylward, Stephen, editor, Zhu, Hongtu, editor, Oguz, Ipek, editor, Yap, Pew-Thian, editor, and Shen, Dinggang, editor

Published
2017
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39. RF Ultrasound Distribution-Based Confidence Maps

Author

Klein, Tassilo, Wells, William M., III, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Navab, Nassir, editor, Hornegger, Joachim, editor, Wells, William M., editor, and Frangi, Alejandro, editor

Published
2015
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40. Hybrid Utrasound and MRI Acquisitions for High-Speed Imaging of Respiratory Organ Motion

Author

Preiswerk, Frank, Toews, Matthew, Hoge, W. Scott, Chiou, Jr-yuan George, Panych, Lawrence P., Wells, William M., III, Madore, Bruno, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Navab, Nassir, editor, Hornegger, Joachim, editor, Wells, William M., editor, and Frangi, Alejandro, editor

Published
2015
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42. Low-Dimensional Statistics of Anatomical Variability via Compact Representation of Image Deformations

Author

Zhang, Miaomiao, Wells, William M., III, Golland, Polina, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Weikum, Gerhard, Series Editor, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Ourselin, Sebastien, editor, Joskowicz, Leo, editor, Sabuncu, Mert R., editor, Unal, Gozde, editor, and Wells, William, editor

Published
2016
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46. Feature-Based Alignment of Volumetric Multi-modal Images

Author

Toews, Matthew, Zöllei, Lilla, Wells, William M., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Gee, James C., editor, Joshi, Sarang, editor, Pohl, Kilian M., editor, Wells, William M., editor, and Zöllei, Lilla, editor

Published
2013
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47. Multinomial Probabilistic Fiber Representation for Connectivity Driven Clustering

Author

Tunç, Birkan, Smith, Alex R., Wasserman, Demian, Pennec, Xavier, Wells, William M., Verma, Ragini, Pohl, Kilian M., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Gee, James C., editor, Joshi, Sarang, editor, Pohl, Kilian M., editor, Wells, William M., editor, and Zöllei, Lilla, editor

Published
2013
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48. Tractography-Driven Groupwise Multi-scale Parcellation of the Cortex

Author

Parisot, Sarah, Arslan, Salim, Passerat-Palmbach, Jonathan, Wells, William M., III, Rueckert, Daniel, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Ourselin, Sebastien, editor, Alexander, Daniel C., editor, Westin, Carl-Fredrik, editor, and Cardoso, M. Jorge, editor

Published
2015
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49. A Feature-Based Approach to Big Data Analysis of Medical Images

Author

Toews, Matthew, Wachinger, Christian, Estepar, Raul San Jose, Wells, William M., III, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Ourselin, Sebastien, editor, Alexander, Daniel C., editor, Westin, Carl-Fredrik, editor, and Cardoso, M. Jorge, editor

Published
2015
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50. Peak learning of mass spectrometry imaging data using artificial neural networks

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Abdelmoula, Walid M, Lopez, Begona Gimenez-Cassina, Randall, Elizabeth C, Kapur, Tina, Sarkaria, Jann N, White, Forest M, Agar, Jeffrey N, Wells, William M, Agar, Nathalie YR, Massachusetts Institute of Technology. Department of Biological Engineering, Abdelmoula, Walid M, Lopez, Begona Gimenez-Cassina, Randall, Elizabeth C, Kapur, Tina, Sarkaria, Jann N, White, Forest M, Agar, Jeffrey N, Wells, William M, and Agar, Nathalie YR

Abstract

AbstractMass spectrometry imaging (MSI) is an emerging technology that holds potential for improving, biomarker discovery, metabolomics research, pharmaceutical applications and clinical diagnosis. Despite many solutions being developed, the large data size and high dimensional nature of MSI, especially 3D datasets, still pose computational and memory complexities that hinder accurate identification of biologically relevant molecular patterns. Moreover, the subjectivity in the selection of parameters for conventional pre-processing approaches can lead to bias. Therefore, we assess if a probabilistic generative model based on a fully connected variational autoencoder can be used for unsupervised analysis and peak learning of MSI data to uncover hidden structures. The resulting msiPL method learns and visualizes the underlying non-linear spectral manifold, revealing biologically relevant clusters of tissue anatomy in a mouse kidney and tumor heterogeneity in human prostatectomy tissue, colorectal carcinoma, and glioblastoma mouse model, with identification of underlying m/z peaks. The method is applied for the analysis of MSI datasets ranging from 3.3 to 78.9 GB, without prior pre-processing and peak picking, and acquired using different mass spectrometers at different centers.

Published
2023

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