Search Results - "Joel Saltz"

Patch-Based Convolutional Neural Network for Whole Slide Tissue Image Classification by Le Hou, Samaras, Dimitris, Kurc, Tahsin M., Yi Gao, Davis, James E., Saltz, Joel H.

“…Convolutional Neural Networks (CNN) are state-of-theart models for many image classification tasks. However, to recognize cancer subtypes automatically,…”
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Robust Histopathology Image Analysis: To Label or to Synthesize? by Hou, Le, Agarwal, Ayush, Samaras, Dimitris, Kurc, Tahsin M., Gupta, Rajarsi R., Saltz, Joel H.

“…Detection, segmentation and classification of nuclei are fundamental analysis operations in digital pathology. Existing state-of-the-art approaches demand…”
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PanCancer insights from The Cancer Genome Atlas: the pathologist's perspective by Cooper, Lee AD, Demicco, Elizabeth G, Saltz, Joel H, Powell, Reid T, Rao, Arvind, Lazar, Alexander J

“…The Cancer Genome Atlas (TCGA) represents one of several international consortia dedicated to performing comprehensive genomic and epigenomic analyses of…”
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AI in Medical Imaging Informatics: Current Challenges and Future Directions by Panayides, Andreas S., Amini, Amir, Filipovic, Nenad D., Sharma, Ashish, Tsaftaris, Sotirios A., Young, Alistair, Foran, David, Do, Nhan, Golemati, Spyretta, Kurc, Tahsin, Huang, Kun, Nikita, Konstantina S., Veasey, Ben P., Zervakis, Michalis, Saltz, Joel H., Pattichis, Constantinos S.

“…This paper reviews state-of-the-art research solutions across the spectrum of medical imaging informatics, discusses clinical translation, and provides future…”
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The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment by Haendel, Melissa A, Chute, Christopher G, Bennett, Tellen D, Eichmann, David A, Guinney, Justin, Kibbe, Warren A, Payne, Philip R O, Pfaff, Emily R, Robinson, Peter N, Saltz, Joel H, Spratt, Heidi, Suver, Christine, Wilbanks, John, Wilcox, Adam B, Williams, Andrew E, Wu, Chunlei, Blacketer, Clair, Bradford, Robert L, Cimino, James J, Clark, Marshall, Colmenares, Evan W, Francis, Patricia A, Gabriel, Davera, Graves, Alexis, Hemadri, Raju, Hong, Stephanie S, Hripscak, George, Jiao, Dazhi, Klann, Jeffrey G, Kostka, Kristin, Lee, Adam M, Lehmann, Harold P, Lingrey, Lora, Miller, Robert T, Morris, Michele, Murphy, Shawn N, Natarajan, Karthik, Palchuk, Matvey B, Sheikh, Usman, Solbrig, Harold, Visweswaran, Shyam, Walden, Anita, Walters, Kellie M, Weber, Griffin M, Zhang, Xiaohan Tanner, Zhu, Richard L, Amor, Benjamin, Girvin, Andrew T, Manna, Amin, Qureshi, Nabeel, Kurilla, Michael G, Michael, Sam G, Portilla, Lili M, Rutter, Joni L, Austin, Christopher P, Gersing, Ken R

“…Abstract Objective Coronavirus disease 2019 (COVID-19) poses societal challenges that require expeditious data and knowledge sharing. Though organizational…”
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State of machine and deep learning in histopathological applications in digestive diseases by Kobayashi, Soma, Saltz, Joel H, Yang, Vincent W

“…Machine learning (ML)- and deep learning (DL)-based imaging modalities have exhibited the capacity to handle extremely high dimensional data for a number of…”
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Sparse autoencoder for unsupervised nucleus detection and representation in histopathology images by Hou, Le, Nguyen, Vu, Kanevsky, Ariel B., Samaras, Dimitris, Kurc, Tahsin M., Zhao, Tianhao, Gupta, Rajarsi R., Gao, Yi, Chen, Wenjin, Foran, David, Saltz, Joel H.

“…We propose a sparse Convolutional Autoencoder (CAE) for simultaneous nucleus detection and feature extraction in histopathology tissue images. Our CAE detects…”
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Caveats for the Use of Operational Electronic Health Record Data in Comparative Effectiveness Research by Hersh, William R., Weiner, Mark G., Embi, Peter J., Logan, Judith R., Payne, Philip R.O., Bernstam, Elmer V., Lehmann, Harold P., Hripcsak, George, Hartzog, Timothy H., Cimino, James J., Saltz, Joel H.

“…The growing amount of data in operational electronic health record systems provides unprecedented opportunity for its reuse for many tasks, including…”
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Deep learning-based approach to the characterization and quantification of histopathology in mouse models of colitis by Kobayashi, Soma, Shieh, Jason, Ruiz de Sabando, Ainara, Kim, Julie, Liu, Yang, Zee, Sui Y, Prasanna, Prateek, Bialkowska, Agnieszka B, Saltz, Joel H, Yang, Vincent W

“…Inflammatory bowel disease (IBD) is a chronic immune-mediated disease of the gastrointestinal tract. While therapies exist, response can be limited within the…”
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Machine-based morphologic analysis of glioblastoma using whole-slide pathology images uncovers clinically relevant molecular correlates by Kong, Jun, Cooper, Lee A D, Wang, Fusheng, Gao, Jingjing, Teodoro, George, Scarpace, Lisa, Mikkelsen, Tom, Schniederjan, Matthew J, Moreno, Carlos S, Saltz, Joel H, Brat, Daniel J

“…Pathologic review of tumor morphology in histologic sections is the traditional method for cancer classification and grading, yet human review has limitations…”
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Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data by Gutman, David A, Cobb, Jake, Somanna, Dhananjaya, Park, Yuna, Wang, Fusheng, Kurc, Tahsin, Saltz, Joel H, Brat, Daniel J, Cooper, Lee A D

“…The integration and visualization of multimodal datasets is a common challenge in biomedical informatics. Several recent studies of The Cancer Genome Atlas…”
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Computational immunohistochemical mapping adds immune context to histological phenotypes in mouse models of colitis by Kobayashi, Soma, Sullivan, Christopher, Bialkowska, Agnieszka B., Saltz, Joel H., Yang, Vincent W.

“…Inflammatory bowel disease (IBD) is characterized by chronic, dysregulated inflammation in the gastrointestinal tract. The heterogeneity of IBD is reflected…”
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Identifying risk of opioid use disorder for patients taking opioid medications with deep learning by Dong, Xinyu, Deng, Jianyuan, Rashidian, Sina, Abell-Hart, Kayley, Hou, Wei, Rosenthal, Richard N, Saltz, Mary, Saltz, Joel H, Wang, Fusheng

“…Abstract Objective The United States is experiencing an opioid epidemic. In recent years, there were more than 10 million opioid misusers aged 12 years or…”
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The proneural molecular signature is enriched in oligodendrogliomas and predicts improved survival among diffuse gliomas by Cooper, Lee A D, Gutman, David A, Long, Qi, Johnson, Brent A, Cholleti, Sharath R, Kurc, Tahsin, Saltz, Joel H, Brat, Daniel J, Moreno, Carlos S

“…The Cancer Genome Atlas Project (TCGA) has produced an extensive collection of '-omic' data on glioblastoma (GBM), resulting in several key insights on…”
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ChampKit: A framework for rapid evaluation of deep neural networks for patch-based histopathology classification by Kaczmarzyk, Jakub R., Gupta, Rajarsi, Kurc, Tahsin M., Abousamra, Shahira, Saltz, Joel H., Koo, Peter K.

“…•We present ChampKit, a Python-based software package that enables rapid exploration and evaluation of deep learning models for patch-level classification of…”
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The Tumor Microenvironment Strongly Impacts Master Transcriptional Regulators and Gene Expression Class of Glioblastoma by Cooper, Lee A.D, Gutman, David A, Chisolm, Candace, Appin, Christina, Kong, Jun, Rong, Yuan, Kurc, Tahsin, Van Meir, Erwin G, Saltz, Joel H, Moreno, Carlos S, Brat, Daniel J

“…The Cancer Genome Atlas (TCGA) project has generated gene expression data that divides glioblastoma (GBM) into four transcriptional classes: proneural, neural,…”
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Methods for Segmentation and Classification of Digital Microscopy Tissue Images by Vu, Quoc Dang, Graham, Simon, Kurc, Tahsin, To, Minh Nguyen Nhat, Shaban, Muhammad, Qaiser, Talha, Koohbanani, Navid Alemi, Khurram, Syed Ali, Kalpathy-Cramer, Jayashree, Zhao, Tianhao, Gupta, Rajarsi, Kwak, Jin Tae, Rajpoot, Nasir, Saltz, Joel, Farahani, Keyvan

“…High-resolution microscopy images of tissue specimens provide detailed information about the morphology of normal and diseased tissue. Image analysis of tissue…”
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Twenty Years of Digital Pathology: An Overview of the Road Travelled, What is on the Horizon, and the Emergence of Vendor-Neutral Archives by Pantanowitz, Liron, Sharma, Ashish, Carter, Alexis B., Kurc, Tahsin, Sussman, Alan, Saltz, Joel

“…Almost 20 years have passed since the commercial introduction of whole-slide imaging (WSI) scanners. During this time, the creation of various WSI devices with…”
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Predicting opioid overdose risk of patients with opioid prescriptions using electronic health records based on temporal deep learning by Dong, Xinyu, Deng, Jianyuan, Hou, Wei, Rashidian, Sina, Rosenthal, Richard N., Saltz, Mary, Saltz, Joel H., Wang, Fusheng

“…[Display omitted] •We train a model to predict opioid overdose in the future based on past electronic health records.•The model is neural network based and…”
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Multi-Class Cell Detection Using Spatial Context Representation by Abousamra, Shahira, Belinsky, David, Van Arnam, John, Allard, Felicia, Yee, Eric, Gupta, Rajarsi, Kurc, Tahsin, Samaras, Dimitris, Saltz, Joel, Chen, Chao

“…In digital pathology, both detection and classification of cells are important for automatic diagnostic and prognostic tasks. Classifying cells into subtypes,…”
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