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1,359 results on '"Tannenbaum, Allen"'

104. Wasserstein HOG: Local Directionality Extraction via Optimal Transport

Author

Zhu, Jiening, Veeraraghavan, Harini, Jiang, Jue, Oh, Jung Hun, Norton, Larry, Deasy, Joseph O., and Tannenbaum, Allen

Abstract

Directionally sensitive radiomic features including the histogram of oriented gradient (HOG) have been shown to provide objective and quantitative measures for predicting disease outcomes in multiple cancers. However, radiomic features are sensitive to imaging variabilities including acquisition differences, imaging artifacts and noise, making them impractical for using in the clinic to inform patient care. We treat the problem of extracting robust local directionality features by mapping via optimal transport a given local image patch to an iso-intense patch of its mean. We decompose the transport map into sub-work costs each transporting in different directions. To test our approach, we evaluated the ability of the proposed approach to quantify tumor heterogeneity from magnetic resonance imaging (MRI) scans of brain glioblastoma multiforme, computed tomography (CT) scans of head and neck squamous cell carcinoma as well as longitudinal CT scans in lung cancer patients treated with immunotherapy. By considering the entropy difference of the extracted local directionality within tumor regions, we found that patients with higher entropy in their images, had significantly worse overall survival for all three datasets, which indicates that tumors that have images exhibiting flows in many directions may be more malignant. This may seem to reflect high tumor histologic grade or disorganization. Furthermore, by comparing the changes in entropy longitudinally using two imaging time points, we found patients with reduction in entropy from baseline CT are associated with longer overall survival (hazard ratio = 1.95, 95% confidence interval of 1.4-2.8, ${p}$ = 1.65e-5). The proposed method provides a robust, training free approach to quantify the local directionality contained in images.

Published
2024
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112. The choroid plexus links innate immunity to CSF dysregulation in hydrocephalus

Author

Robert, Stephanie M., primary, Reeves, Benjamin C., additional, Kiziltug, Emre, additional, Duy, Phan Q., additional, Karimy, Jason K., additional, Mansuri, M. Shahid, additional, Marlier, Arnaud, additional, Allington, Garrett, additional, Greenberg, Ana B.W., additional, DeSpenza, Tyrone, additional, Singh, Amrita K., additional, Zeng, Xue, additional, Mekbib, Kedous Y., additional, Kundishora, Adam J., additional, Nelson-Williams, Carol, additional, Hao, Le Thi, additional, Zhang, Jinwei, additional, Lam, TuKiet T., additional, Wilson, Rashaun, additional, Butler, William E., additional, Diluna, Michael L., additional, Feinberg, Philip, additional, Schafer, Dorothy P., additional, Movahedi, Kiavash, additional, Tannenbaum, Allen, additional, Koundal, Sunil, additional, Chen, Xinan, additional, Benveniste, Helene, additional, Limbrick, David D., additional, Schiff, Steven J., additional, Carter, Bob S., additional, Gunel, Murat, additional, Simard, J. Marc, additional, Lifton, Richard P., additional, Alper, Seth L., additional, Delpire, Eric, additional, and Kahle, Kristopher T., additional

Published
2023
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117. Regularized Optimal Mass Transport with Nonlinear Diffusion

Author

Xu, Kaiming, Chen, Xinan, Benveniste, Helene, and Tannenbaum, Allen

Subjects
Fluid Dynamics (physics.flu-dyn), FOS: Physical sciences, Physics - Fluid Dynamics, Medical Physics (physics.med-ph), Physics - Medical Physics
Abstract

In this paper, we combine nonlinear diffusion with the regularized optimal mass transport (rOMT) model. As we will demonstrate, this new approach provides further insights into certain applications of fluid flow analysis in the brain. From the point of view of image processing, the anisotropic diffusion method, based on Perona-Malik, explicitly considers edge information. Applied to rOMT analysis of glymphatic transport based on DCE-MRI data, this new framework appears to capture a larger advection-dominant volume.

Published
2023
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118. Negative probabilities in Gene Regulatory Networks

Author

Dong, Anqi, Georgiou, Tryphon T., and Tannenbaum, Allen

Subjects
FOS: Computer and information sciences, Computer Science - Machine Learning, 92F99, 49M29, 90C30, 93-08, 90C25, Molecular Networks (q-bio.MN), FOS: Biological sciences, FOS: Electrical engineering, electronic engineering, information engineering, Quantitative Biology - Molecular Networks, Systems and Control (eess.SY), Electrical Engineering and Systems Science - Systems and Control, Machine Learning (cs.LG)
Abstract

We introduce a natural framework to identify sign-indefinite co-expressions between genes based on the known expressions and given the sign of their respective correlations. Specifically, given information concerning the affinity among genes (i.e., connectivity in the gene regulatory network) and knowledge whether they promote/inhibit co-expression of the respective protein production, we seek rates that may explain the observed stationary distributions at the level of proteins. We propose to encapsulate their ``promotion vs.\ inhibition'' functionality in a sign-indefinite probability transition matrix--a matrix whose row-sums equal to one, but is otherwise sign indefinite. The purpose of constructing such a representation for the interaction network with sign-indefinite contributions in protein regulation, is to quantify the structure and significance of various links, and to explain how these may affect the geometry of the network, highlighting the significance of the regulatory functions of certain genes. We cast the problem of finding the interaction (sign-indefinite) transition matrix as a solution to a convex optimization problem from which all the relevant geometric properties may be easily derived., Comment: 6 pages

Published
2023
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124. Improved prediction of drug-induced liver injury literature using natural language processing and machine learning methods.

Author

Jung Hun Oh, Tannenbaum, Allen, and Deasy, Joseph O.

Subjects
MACHINE learning, SCIENTIFIC literature, LIVER injuries, PROGRAMMING languages, DRUG side effects, NATURAL language processing
Abstract

Drug-induced liver injury (DILI) is an adverse hepatic drug reaction that can potentially lead to life-threatening liver failure. Previously published work in the scientific literature on DILI has provided valuable insights for the understanding of hepatotoxicity as well as drug development. However, the manual search of scientific literature in PubMed is laborious and time-consuming. Natural language processing (NLP) techniques along with artificial intelligence/machine learning approaches may allow for automatic processing in identifying DILIrelated literature, but useful methods are yet to be demonstrated. To address this issue, we have developed an integrated NLP/machine learning classification model to identify DILI-related literature using only paper titles and abstracts. For prediction modeling, we used 14,203 publications provided by the Critical Assessment of Massive Data Analysis (CAMDA) challenge, employing word vectorization techniques in NLP in conjunction with machine learning methods. Classification modeling was performed using 2/3 of the data for training and the remainder for test in internal validation. The best performance was achieved using a linear support vector machine (SVM) model on the combined vectors derived from term frequency-inverse document frequency (TF-IDF) and Word2Vec, resulting in an accuracy of 95.0% and an F1-score of 95.0%. The final SVM model constructed from all 14,203 publications was tested on independent datasets, resulting in accuracies of 92.5%, 96.3%, and 98.3%, and F1-scores of 93.5%, 86.1%, and 75.6% for three test sets (T1-T3). Furthermore, the SVM model was tested on four external validation sets (V1-V4), resulting in accuracies of 92.0%, 96.2%, 98.3%, and 93.1%, and F1-scores of 92.4%, 82.9%, 75.0%, and 93.3%. [ABSTRACT FROM AUTHOR]

Published
2023
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128. Changes in the geometry and robustness of diffusion tensor imaging networks: Secondary analysis from a randomized controlled trial of young autistic children receiving an umbilical cord blood infusion

Author

Simhal, Anish K., primary, Carpenter, Kimberly L. H., additional, Kurtzberg, Joanne, additional, Song, Allen, additional, Tannenbaum, Allen, additional, Zhang, Lijia, additional, Sapiro, Guillermo, additional, and Dawson, Geraldine, additional

Published
2022
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129. Remembrances of Ciprian Ilie Foias

Author

Becker, Robert A, primary, Bercovici, Hari, additional, Biswas, Animikh, additional, Cheskidov, Alexey, additional, Constantin, Peter, additional, Eden, Alp, additional, Frazho, Art, additional, Jolly, Michael, additional, Kukavica, Igor, additional, Pearcy, Carl, additional, Rosa, Ricardo M S, additional, Saut, Jean-Claude, additional, Tannenbaum, Allen, additional, Temam, Roger, additional, Titi, Edriss, additional, and Voiculescu, Dan, additional

Published
2022
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134. Simultaneous Multi-object Segmentation Using Local Robust Statistics and Contour Interaction

Author

Gao, Yi, Tannenbaum, Allen, Kikinis, Ron, 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, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Menze, Bjoern, editor, Langs, Georg, editor, Tu, Zhuowen, editor, and Criminisi, Antonio, editor

Published
2011
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142. Robust 3D Pose Estimation and Efficient 2D Region-Based Segmentation from a 3D Shape Prior

Author

Dambreville, Samuel, Sandhu, Romeil, Yezzi, Anthony, Tannenbaum, Allen, 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, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Forsyth, David, editor, Torr, Philip, editor, and Zisserman, Andrew, editor

Published
2008
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143. Label Space: A Coupled Multi-shape Representation

Author

Malcolm, James, Rathi, Yogesh, Shenton, Martha E., Tannenbaum, Allen, 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, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Metaxas, Dimitris, editor, Axel, Leon, editor, Fichtinger, Gabor, editor, and Székely, Gábor, editor

Published
2008
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144. Label Space: A Multi-object Shape Representation

Author

Malcolm, James, Rathi, Yogesh, Tannenbaum, Allen, 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, Brimkov, Valentin E., editor, Barneva, Reneta P., editor, and Hauptman, Herbert A., editor

Published
2008
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145. Finsler Tractography for White Matter Connectivity Analysis of the Cingulum Bundle

Author

Melonakos, John, Mohan, Vandana, Niethammer, Marc, Smith, Kate, Kubicki, Marek, Tannenbaum, Allen, 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, Ayache, Nicholas, editor, Ourselin, Sébastien, editor, and Maeder, Anthony, editor

Published
2007
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148. Comparative Analysis of Kernel Methods for Statistical Shape Learning

Author

Rathi, Yogesh, Dambreville, Samuel, Tannenbaum, Allen, 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, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Beichel, Reinhard R., editor, and Sonka, Milan, editor

Published
2006
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149. Particle Filtering with Dynamic Shape Priors

Author

Rathi, Yogesh, Dambreville, Samuel, Tannenbaum, Allen, 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, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Campilho, Aurélio, editor, and Kamel, Mohamed S., editor

Published
2006
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150. A Shape-Based Approach to Robust Image Segmentation

Author

Dambreville, Samuel, Rathi, Yogesh, Tannenbaum, Allen, 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, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Campilho, Aurélio, editor, and Kamel, Mohamed S., editor

Published
2006
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