Albumentations: Fast and Flexible Image Augmentations
Buslaev, Alexander, Iglovikov, Vladimir I., Khvedchenya, Eugene, Parinov, Alex, Druzhinin, Mikhail, Kalinin, Alexandr A.
Published in Information (Basel) (01.02.2020)
Published in Information (Basel) (01.02.2020)
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Journal Article
Deep learning in pharmacogenomics: from gene regulation to patient stratification
Kalinin, Alexandr A, Higgins, Gerald A, Reamaroon, Narathip, Soroushmehr, Sayedmohammadreza, Allyn-Feuer, Ari, Dinov, Ivo D, Najarian, Kayvan, Athey, Brian D
Published in Pharmacogenomics (01.05.2018)
Published in Pharmacogenomics (01.05.2018)
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Journal Article
Ten quick tips for deep learning in biology
Lee, Benjamin D, Gitter, Anthony, Greene, Casey S, Raschka, Sebastian, Maguire, Finlay, Titus, Alexander J, Kessler, Michael D, Lee, Alexandra J, Chevrette, Marc G, Stewart, Paul Allen, Britto-Borges, Thiago, Cofer, Evan M, Yu, Kun-Hsing, Carmona, Juan Jose, Fertig, Elana J, Kalinin, Alexandr A, Signal, Brandon, Lengerich, Benjamin J, Triche, Jr, Timothy J, Boca, Simina M
Published in PLoS computational biology (01.03.2022)
Published in PLoS computational biology (01.03.2022)
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Journal Article
SOCRAT: a Dynamic Web Toolbox for Interactive Data Processing, Analysis and Visualization
Kalinin, Alexandr A, Palanimalai, Selvam, Zhu, Junqi, Wu, Wenyi, Devraj, Nikhil, Ye, Chunchun, Ponarul, Nellie, Husain, Syed S, Dinov, Ivo D
Published in Information (Basel) (01.11.2022)
Published in Information (Basel) (01.11.2022)
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Journal Article
3D convolutional neural networks for stalled brain capillary detection
Solovyev, Roman, Kalinin, Alexandr A., Gabruseva, Tatiana
Published in Computers in biology and medicine (01.02.2022)
Published in Computers in biology and medicine (01.02.2022)
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Journal Article
Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations
Chandrasekaran, Srinivas Niranj, Cimini, Beth A, Goodale, Amy, Miller, Lisa, Kost-Alimova, Maria, Jamali, Nasim, Doench, John G, Fritchman, Briana, Skepner, Adam, Melanson, Michelle, Kalinin, Alexandr A, Arevalo, John, Haghighi, Marzieh, Caicedo, Juan C, Kuhn, Daniel, Hernandez, Desiree, Berstler, James, Shafqat-Abbasi, Hamdah, Root, David E, Swalley, Susanne E, Garg, Sakshi, Singh, Shantanu, Carpenter, Anne E
Published in Nature methods (01.06.2024)
Published in Nature methods (01.06.2024)
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Journal Article
Integrating inflammatory biomarker analysis and artificial-intelligence-enabled image-based profiling to identify drug targets for intestinal fibrosis
Yu, Shan, Kalinin, Alexandr A., Paraskevopoulou, Maria D., Maruggi, Marco, Cheng, Jie, Tang, Jie, Icke, Ilknur, Luo, Yi, Wei, Qun, Scheibe, Dan, Hunter, Joel, Singh, Shantanu, Nguyen, Deborah, Carpenter, Anne E., Horman, Shane R.
Published in Cell chemical biology (21.09.2023)
Published in Cell chemical biology (21.09.2023)
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Journal Article
Hypothesis: Caco‐2 cell rotational 3D mechanogenomic turing patterns have clinical implications to colon crypts
Zheng, Gen, Kalinin, Alexandr A., Dinov, Ivo D., Meixner, Walter, Zhu, Shengtao, Wiley, John W.
Published in Journal of cellular and molecular medicine (01.12.2018)
Published in Journal of cellular and molecular medicine (01.12.2018)
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Journal Article
3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification
Kalinin, Alexandr A, Allyn-Feuer, Ari, Ade, Alex, Fon, Gordon-Victor, Meixner, Walter, Dilworth, David, Husain, Syed S, de Wet, Jeffrey R, Higgins, Gerald A, Zheng, Gen, Creekmore, Amy, Wiley, John W, Verdone, James E, Veltri, Robert W, Pienta, Kenneth J, Coffey, Donald S, Athey, Brian D, Dinov, Ivo D
Published in Scientific reports (12.09.2018)
Published in Scientific reports (12.09.2018)
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Journal Article
Publisher Correction: 3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification
Kalinin, Alexandr A, Allyn-Feuer, Ari, Ade, Alex, Fon, Gordon-Victor, Meixner, Walter, Dilworth, David, Husain, Syed S, de Wet, Jeffrey R, Higgins, Gerald A, Zheng, Gen, Creekmore, Amy, Wiley, John W, Verdone, James E, Veltri, Robert W, Pienta, Kenneth J, Coffey, Donald S, Athey, Brian D, Dinov, Ivo D
Published in Scientific reports (26.10.2018)
Published in Scientific reports (26.10.2018)
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Journal Article
Improving Acne Image Grading with Label Distribution Smoothing
Prokhorov, Kirill, Kalinin, Alexandr A.
Published in 2024 IEEE International Symposium on Biomedical Imaging (ISBI) (27.05.2024)
Published in 2024 IEEE International Symposium on Biomedical Imaging (ISBI) (27.05.2024)
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Conference Proceeding
Breast Tumor Cellularity Assessment Using Deep Neural Networks
Rakhlin, Alexander, Tiulpin, Aleksei, Shvets, Alexey A., Kalinin, Alexandr A., Iglovikov, Vladimir I., Nikolenko, Sergey
Published in 2019 IEEE/CVF International Conference on Computer Vision Workshop (ICCVW) (01.10.2019)
Published in 2019 IEEE/CVF International Conference on Computer Vision Workshop (ICCVW) (01.10.2019)
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Conference Proceeding
SOCRAT Platform Design: A Web Architecture for Interactive Visual Analytics Applications
Kalinin, Alexandr A, Palanimalai, Selvam, Dinov, Ivo D
Published in Proceedings of the 2nd Workshop on Human-In-the-Loop Data Analytics. Workshop on Human-In-the-Loop Data Analytics (2nd : 2017 : Chicago, Ill.) (01.04.2017)
Published in Proceedings of the 2nd Workshop on Human-In-the-Loop Data Analytics. Workshop on Human-In-the-Loop Data Analytics (2nd : 2017 : Chicago, Ill.) (01.04.2017)
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Journal Article
Opportunities and obstacles for deep learning in biology and medicine
Ching, Travers, Himmelstein, Daniel S., Beaulieu-Jones, Brett K., Kalinin, Alexandr A., Do, Brian T., Way, Gregory P., Ferrero, Enrico, Agapow, Paul-Michael, Zietz, Michael, Hoffman, Michael M., Xie, Wei, Rosen, Gail L., Lengerich, Benjamin J., Israeli, Johnny, Lanchantin, Jack, Woloszynek, Stephen, Carpenter, Anne E., Shrikumar, Avanti, Xu, Jinbo, Cofer, Evan M., Lavender, Christopher A., Turaga, Srinivas C., Alexandari, Amr M., Lu, Zhiyong, Harris, David J., DeCaprio, Dave, Qi, Yanjun, Kundaje, Anshul, Peng, Yifan, Wiley, Laura K., Segler, Marwin H. S., Boca, Simina M., Swamidass, S. Joshua, Huang, Austin, Gitter, Anthony, Greene, Casey S.
Published in Journal of the Royal Society interface (01.04.2018)
Published in Journal of the Royal Society interface (01.04.2018)
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Journal Article
Automatic Instrument Segmentation in Robot-Assisted Surgery using Deep Learning
Shvets, Alexey A., Rakhlin, Alexander, Kalinin, Alexandr A., Iglovikov, Vladimir I.
Published in 2018 17th IEEE International Conference on Machine Learning and Applications (ICMLA) (01.12.2018)
Published in 2018 17th IEEE International Conference on Machine Learning and Applications (ICMLA) (01.12.2018)
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Conference Proceeding
3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification
Kalinin, Alexandr A, Allyn-Feuer, Ari, Ade, Alex, Gordon-Victor Fon, Meixner, Walter, Dilworth, David, Husain, Syed S, De Wet, Jeffrey R, Higgins, Gerald A, Zheng, Gen, Creekmore, Amy, Wiley, John W, Verdone, James E, Veltri, Robert W, Pienta, Kenneth J, Coffey, Donald S, Athey, Brian D, Dinov, Ivo D
Published in bioRxiv (08.08.2018)
Published in bioRxiv (08.08.2018)
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Paper
Angiodysplasia Detection and Localization Using Deep Convolutional Neural Networks
Shvets, Alexey A., Iglovikov, Vladimir I., Rakhlin, Alexander, Kalinin, Alexandr A.
Published in 2018 17th IEEE International Conference on Machine Learning and Applications (ICMLA) (01.12.2018)
Published in 2018 17th IEEE International Conference on Machine Learning and Applications (ICMLA) (01.12.2018)
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Conference Proceeding