Publications

For an up-to-date list of publication, see my Google scholar profile.

Publications

Deep learning-based survival prediction for multiple cancer types using histopathology images. Ellery Wulczyn, David F. Steiner, Zhaoyang Xu, Apaar Sadhwani, Hongwu Wang, Isabelle Flament, Craig H. Mermel, Po-Hsuan Cameron Chen, Yun Liu, Martin C. Stumpe. PLoS ONE 15(6) e0233678 (2020)

also: arXiv preprint: 1912.07354 (2019)

Prediction of mortality from 12-lead electrocardiogram voltage data using a deep neural network. Sushravya Raghunath, Alvaro E. Ulloa Cerna, Linyuan Jing, David P. vanMaanen, Joshua Stough, Dustin N. Hartzel, Joseph B. Leader, H. Lester Kirchner, Martin C. Stumpe, Ashraf Hafez, Arun Nemani, Tanner Carbonati, Kipp W. Johnson, Katelyn Young, Christopher W. Good, John M. Pfeifer, Aalpen A. Patel, Brian P. Delisle, Amro Alsaid, Dominik Beer, Christopher M. Haggerty & Brandon K. Fornwalt. Nature Medicine, https://doi.org/10.1038/s41591-020-0870-z (2020)

Whole-Slide Image Focus Quality: Automatic Assessment and Impact on AI Cancer Detection. Timo Kohlberger, Yun Liu, Melissa Moran, Po-Hsuan (Cameron) Chen, Trissia Brown, Jason D. Hipp, Craig H. Mermel, Martin C. Stumpe. J Pathol Inform, 10:39 (2019)

also: arXiv preprint: 1901.04619 (2019)

An Augmented Reality Microscope with Real-time Artificial Intelligence Integration. Po-Hsuan (Cameron) Chen, Krishna Gadepalli, Robert MacDonald, Yun Liu, Shiro Kadowaki, Kunal Nagpal, Timo Kohlberger, Jeffrey Dean, Greg S. Corrado, Jason D. Hipp, Martin C. Stumpe. Nature Medicine, volume 25, pages 1453–1457 (2019)

also: arXiv preprint: 1812.00825 (2018)

Artificial Intelligence–Based Breast Cancer Nodal Metastasis Detection - Insights Into the Black Box for Pathologists. Yun Liu, Timo Kohlberger, Mohammad Norouzi, George E. Dahl, Jenny L. Smith, Arash Mohtashamian, Niels Olson, Lily H. Peng, Jason D. Hipp, Martin C. Stumpe. Arch Pathol Lab Med.: July 2019, Vol. 143, No. 7, pp. 859-868

Similar Image Search for Histopathology: SMILY. Narayan Hegde, Jason D. Hipp, Yun Liu, Michael E. Buck, Emily Reif, Daniel Smilkov, Michael Terry, Carrie J. Cai, Mahul B. Amin, Craig H. Mermel, Phil Q. Nelson, Lily H. Peng, Greg S. Corrado, Martin C. Stumpe. Nature Digital Medicine, volume 2, Article number: 56 (2019)

also: arXiv preprint: 1901.11112 (2019)

Human-Centered Tools for Coping with Imperfect Algorithms during Medical Decision-Making. Carrie J. Cai, Emily Reif, Narayan Hegde, Jason Hipp, Been Kim, Daniel Smilkov, Martin Wattenberg, Fernanda Viegas, Greg S. Corrado, Martin C. Stumpe, Michael Terry. Proceedings of the 2019 CHI Conference on Human Factors in Computing Systems 2019, DOI: 10.1145/3290605.3300234

also: arXiv preprint: 1902.02960 (2019)

Development and Validation of a Deep Learning Algorithm for Improving Gleason Scoring of Prostate Cancer. Kunal Nagpal, Davis Foote, Yun Liu, Po-Hsuan (Cameron) Chen, Ellery Wulczyn, Fraser Tan, Niels Olson, Jenny L. Smith, Arash Mohtashamian, James H. Wren, Greg S. Corrado, Robert MacDonald, Lily H. Peng, Mahul B. Amin, Andrew J. Evans, Ankur R. Sangoi, Craig H. Mermel, Jason D. Hipp, Martin C. Stumpe. Nature Digital Medicine, volume 2, Article number: 48 (2019)

also: arXiv preprint: 1811.06497 (2018)

Computer‑Aided Laser Dissection: A Microdissection Workflow Leveraging Image Analysis Tools. Jason D. Hipp, Donald J. Johann, Yun Chen, Anant Madabhushi, James Monaco, Jerome Cheng, Jaime Rodriguez‑Canales, Martin C. Stumpe, Greg Riedlinger, Avi Z. Rosenberg, Jeffrey C. Hanson1, Lakshmi P. Kunju, Michael R. Emmert‑Buck, Ulysses J. Balis, Michael A. Tangrea. J Pathol Inform 2018;9:45

Impact of Deep Learning Assistance on the Histopathologic Review of Lymph Nodes for Metastatic Breast Cancer. David F Steiner, Robert MacDonald, Yun Liu, Peter Truszkowski, Jason D Hipp, Christopher Gammage, Florence Thng, Lily Peng, Martin C Stumpe. The American Journal of Surgical Pathology, Volume 42, Issue 12, 1636–1646, 2018

Detecting Cancer Metastases on Gigapixel Pathology Images. Yun Liu, Krishna Gadepalli, Mohammad Norouzi, George E Dahl, Timo Kohlberger, Aleksey Boyko, Subhashini Venugopalan, Aleksei Timofeev, Philip Q Nelson, Greg S Corrado, Jason D Hipp, Lily Peng, Martin C Stumpe. arXiv preprint: 1703.02442 (2017)

Development and validation of a deep learning algorithm for detection of diabetic retinopathy in retinal fundus photographs. Varun Gulshan, Lily Peng, Marc Coram, Martin C Stumpe, Derek Wu, Arunachalam Narayanaswamy, Subhashini Venugopalan, Kasumi Widner, Tom Madams, Jorge Cuadros, Ramasamy Kim, Rajiv Raman, Philip C Nelson, Jessica L Mega, Dale R Webster. JAMA, 316(22), 2402-2410 (2016)

Ontological supervision for fine grained classification of street view storefronts. Yair Movshovitz-Attias, Qian Yu, Martin C Stumpe, Vinay Shet, Sacha Arnoud, Liron Yatziv. Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 1693-1702 (2015)

Large Scale Business Discovery from Street Level Imagery. Qian Yu, Christian Szegedy, Martin C Stumpe, Liron Yatziv, Vinay Shet, Julian Ibarz, Sacha Arnoud. arXiv preprint: 1512.05430 (2015)

Multiscale Systematic Error Correction via Wavelet-Based Bandsplitting in Kepler Data. Martin C. Stumpe, Jeffrey C. Smith, Joseph H. Catanzarite, Jeffrey E. Van Cleve, Jon M. Jenkins, Joseph D. Twicken, Forrest R. Girouard. Publications of the Astronomical Society of the Pacific, 126 (935), 100-114 (2014)

Kepler Presearch Data Conditioning II - A Bayesian Approach to Systematic Error Correction. Jeffrey C. Smith, Martin C. Stumpe, Jeffrey E. Van Cleve, Jon M. Jenkins, Thomas S. Barclay, Michael N. Fanelli, Forrest R. Girouard, Jeffery J. Kolodziejczak, Sean D. McCauliff, Robert L. Morris, Joseph D. Twicken. Publications of the Astronomical Society of the Pacific, 124 (119), 1000-1014 (2012)

Kepler Presearch Data Conditioning I - Architecture and Algorithms for Error Correction in Kepler Light Curves. Martin C. Stumpe, Jeffrey C. Smith, Jeffrey E. Van Cleve, Joseph D. Twicken, Thomas S. Barclay, Michael N. Fanelli, Forrest R. Girouard, Jon M. Jenkins, Jeffery J. Kolodziejczak, Sean D. McCauliff, Robert L. Morris. Publications of the Astronomical Society of the Pacific, 124 (119), 985-999 (2012)

Calculation of Local Water Densities in Biological Systems - A Comparison of Molecular Dynamics Simulations and the 3D-RISM Molecular Theory of Solvation. Martin C. Stumpe, Nikolay Blinov, David Wishart, Andriy Kovalenko, and Vijay S. Pande. J. Phys. Chem. B, 115(2), 319-328 (2011) (Cover article)

Molecular Determinants of Snurportin 1 Ligand Affinity and Structural Response upon Binding. Maik Goette, Martin C. Stumpe, Ralf Ficner, and Helmut Grubmüller. Biophys. J., 97(2), 581-589 (2009)

Urea Impedes the Hydrophobic Collapse of Partially Unfolded Proteins. Martin C. Stumpe and Helmut Grubmüller. Biophys. J., 96(9), 3744-3752 (2009)

Polar or Apolar - The Role of Polarity for Urea-Induced Protein Denaturation. Martin C. Stumpe and Helmut Grubmüller. PLoS Comp. Biol., 4(11), e1000221 (2008)

Interaction of Urea with Amino Acids - Implications for Urea-Induced Protein Denaturation. Martin C. Stumpe and Helmut Grubmüller. J. Am. Chem. Soc., 129(51), 16126-16131 (2007)

Aqueous Urea Solutions: Structure, Energetics, and Urea Aggregation. Martin C. Stumpe and Helmut Grubmüller. J. Phys. Chem. B, 111(22), 6220-6228 (2007) (Cover article)

Reliability of associative recall based on data manipulations in phase encoded volume holographic storage systems. G. Berger, M. Stumpe, M. Höhne, and C. Denz. J. Opt. A: Pure Appl. Opt., 7:567-575 (2005)

Publications (AnTracks collaboration papers)

Social behaviour and collective motion in plant-animal worms. Nigel R Franks, Alan Worley, Katherine AJ Grant, Alice R Gorman, Victoria Vizard, Harriet Plackett, Carolina Doran, Margaret L Gamble, Martin C Stumpe, Ana B Sendova-Franks. Proc. R. Soc. B, 283(1825), 20152946 (2016)

Exploration adjustment by ant colonies. Carolina Doran, Martin C Stumpe, Ana Sendova-Franks, Nigel R Franks. Royal Society open science. 3(1), 150533 (2016)

Collective search by ants in microgravity. Stefanie M Countryman, Martin C Stumpe, Sam P Crow, Frederick R Adler, Michael J Greene, Merav Vonshak, Deborah M Gordon. Frontiers in Ecology and Evolution, 3(25) (2015)

The role of social attraction and its link with boldness in the collective movements of three-spined sticklebacks. Jolle W Jolles, Adeline Fleetwood-Wilson, Shinnosuke Nakayama, Martin C Stumpe, Rufus A Johnstone, Andrea Manica. Animal behaviour, 99, 147-153 (2015)

Ants work harder during consensus decision-making in small groups. Adam L Cronin, Martin C Stumpe. Journal of The Royal Society Interface, 11(98), 20140641 (2014)

The role of previous social experience on risk-taking and leadership in three-spined sticklebacks. Jolle W Jolles, Adeline Fleetwood-Wilson, Shinnosuke Nakayama, Martin C Stumpe, Rufus A Johnstone, Andrea Manica. Behav Ecol (2014) 25 (6): 1395-1401

Experience overrides personality differences in the tendency to follow but not in the tendency to lead. S Nakayama, MC Stumpe, A Manica, RA Johnstone. Proceedings of the Royal Society B: Biological Sciences, 280(1769) 20131724 (2013)

Harvester ants use interactions to regulate forager activation and availability. Pinter-Wollman, Noa; Bala, Ashwin; Merrell, Andrew; Queirolo, Jovel; Stumpe, Martin C; Holmes, Susan; Gordon, Deborah M. Proceedings of the Animal Behaviour, 86(1), 197-207 (2013)

Publications (Kepler long authorlist papers)

Detection of Potential Transit Signals in the First Three Quarters of Kepler Mission Data. Peter Tenenbaum, Jessie L. Christiansen, Jon M. Jenkins, Jason F. Rowe, Shawn Seader, Douglas A. Caldwell, Bruce D. Clarke, Jie Li, Elisa V. Quintana, Jeffrey C. Smith, Martin C. Stumpe, Susan E. Thompson, Joseph D. Twicken, Jeffrey Van Cleve, William J. Borucki, Miles T. Cote, Michael R. Haas, Dwight T. Sanderfer, Forrest R. Girouard, Todd C. Klaus, Christopher K. Middour, Bill Wohler, Natalie M. Batalha, Thomas Barclay, and James E. Nickerson. Astrophysical Journal Supplemental Series, 199, 24 (2012)

Kepler-20: A Sun-like Star with Three Sub-Neptune Exoplanets and Two Earth-Size Candidates. Thomas N. Gautier III, David Charbonneau, Jason F. Rowe, Geoffrey W. Marcy, Howard Isaacson, Guillermo Torres, Francois Fressin, Leslie A. Rogers, Jean-Michel Désert, Lars A. Buchhave, David W. Latham, Samuel N. Quinn, David R. Ciardi, Daniel C. Fabrycky, Eric B. Ford, Ronald L. Gilliland, Lucianne M. Walkowicz, Stephen T. Bryson, William D. Cochran, Michael Endl, Debra A. Fischer, Steve B. Howel, Elliott P. Horch, Thomas Barclay, Natalie Batalha, William J. Borucki, Jessie L. Christiansen, John C. Geary, Christopher E. Henze, Matthew J. Holman, Khadeejah Ibrahim, Jon M. Jenkins, Karen Kinemuchi, David G. Koch, Jack J. Lissauer, Dwight T. Sanderfer, Dimitar D. Sasselov, Sara Seager, Kathryn Silverio, Jeffrey C. Smith, Martin Still, Martin C. Stumpe, Peter Tenenbaum, Jeffrey Van Cleve. Astrophysical Journal, 749, 15 (2012)

Probing the core structure and evolution of red giants using gravity-dominated mixed modes observed with Kepler. B. Mosser, M. J. Goupil, K. Belkacem, E. Michel, D. Stello, J. P. Marques, Y. Elsworth, C. Barban, P. G. Beck, T. R. Bedding, J. De Ridder, R. A. Garcya, S. Hekker, T. Kallinger, R. Samadi, M. C. Stumpe, T. Barclay, and C. J. Burke. Astronomy & Astrophysics, 540, A143 (2012)

Oscillation mode frequencies of 61 main-sequence and subgiant stars observed by Kepler. T. Appourchaux, W. J. Chaplin, R. A. Garcya, M. Gruberbauer, G. A. Verner, H. M. Antia, O. Benomar, T. L. Campante, G. R. Davies, S. Deheuvels, R. Handberg, S. Hekker, R. Howe, C. Regulo, D. Salabert, T. R. Bedding, T. R. White, J. Ballot, S. Mathur, V. Silva Aguirre, Y. P. Elsworth, S. Basu, R. Gilliland, J. Christensen-Dalsgaard, H. Kjeldsen, K. Uddin, M. C. Stumpe, and T. Barclay. Astronomy & Astrophysics, 543 (2012)

Unusual high-frequency oscillations in the Kepler Scuti star KIC 4840675. L. A. Balona, M. Breger, G. Catanzaro, M. S. Cunha, G. Handler, Z. Kolaczkoswki, D. W. Kurtz, S. Murphy, E. Niemczura, M. Paparo, B. Smalley, R. Szabo, K. Uytterhoeven, J. L. Christiansen, K. Uddin, M. C. Stumpe. Monthly Notices of the Royal Astronomical Society, doi: 10.1111/j.1365-2955.2012.2195.x (2012)

Planetary Candidates Observed by Kepler III: Analysis of the First 16 Months of Data. Natalie M. Batalha, Jason F. Rowe, Stephen T. Bryson, Thomas Barclay, Christopher J. Burke, Douglas A. Caldwell, Jessie L. Christiansen, Fergal Mullally, Susan E. Thompson, Timothy M. Brown, Andrea K. Dupree, Daniel C. Fabrycky, Eric B. Ford, Jonathan J. Fortney, Ronald L. Gilliland, Howard Isaacson, David W. Latham, Geoffrey W. Marcy, Samuel Quinn, Darin Ragozzine, Avi Shporer, William J. Borucki, David R. Ciardi, Thomas N. Gautier III, Michael R. Haas, Jon M. Jenkins, David G. Koch, Jack J. Lissauer, William Rapin, Gibor S. Basri, Alan P. Boss, Lars A. Buchhave, David Charbonneau, Joergen Christensen-Dalsgaard, Bruce D. Clarke, William D. Cochran, Brice-Olivier Demory, Edna Devore, Gilbert A. Esquerdo, Mark Everett, Francois Fressin, John C. Geary, Forrest R. Girouard, Alan Gould, Jennifer R. Hall, Matthew J. Holman, Andrew W. Howard, Steve B. Howell, Khadeejah A. Ibrahim, K. Kinemuchi, Hans Kjeldsen, Todd C. Klaus, Jie Li, Philip W. Lucas, Robert L. Morris, Andrej Prsa, Elisa Quintana, Dwight T. Sanderfer, Dimitar Sasselov, Shawn E. Seader, Jeffrey C. Smith, Jason H. Steffen, Martin Still, Martin C. Stumpe, Jill C. Tarter, Peter Tenenbaum, Guillermo Torres, Joseph D. Twicken, Kamal Uddin, Jeffrey Van Cleve, Lucianne Walkowicz, William F. Welsh. Astrophysical Journal Supplemental Series, 204, 24 (2013)

The Derivation, Properties and Value of Kepler's Combined Differential Photometric Precision. Jessie L. Christiansen, Jon M. Jenkins, Thomas S. Barclay, Christopher J. Burke, Douglas A. Caldwell, Bruce D. Clarke, Jie Li, Shawn Seader, Jeffrey C. Smith, Martin C. Stumpe, Peter Tenenbaum, Susan E. Thompson, Joseph D. Twicken, Jeffrey Van Cleve. Publications of the Astronomical Society of the Pacific, 124 (922), 1279-1287 (2012)

Fundamental Properties of Stars Using Asteroseismology From Kepler & Corot and Interferometry from the CHARA Array. D. Huber, M. J. Ireland, T. R. Bedding, I. M. Brandao, V. Maestro, T. R. White, H. Bruntt, L. Casagrande, J. Molenda-Zakowicz, V. Silva Aguirre, T. Barclay, C. Burke, W. J. Chaplin, J. Christensen-Dalsgaard, M. S. Cunha, J. De Ridder, C. D. Farrington, A. Frasca, R. A. Garcia, R. L. Gilliland, P. J. Goldfinger, S. Hekker, S. D. Kawaler, H. Kjeldsen, H. A. McAlister, T. S. Metcalfe, A. Miglio, M.J.P.F.G. Monteiro, M. H. Pinsonneault, G. H. Schaefer, D. Stello, M. C. Stumpe, J. Sturmann, L. Sturmann, T. A. Ten-Brummelaar, N. Turner, K. Uytterhoeven. Astrophysical Journal, 760, 32 (2013)

Book Chapters & Theses

Machine Learning for the Integration of Pathology Images with Molecular Data. Chapter 7 in Pathological Specimens And Genomic Medicine: Emerging Issues. Martin C Stumpe, Arran Schlosberg, Laura Deming, Lily Peng, Graziella Solinas, Jason Hipp. ISBN 978-9814343442, World Scientific (2019).

Chaperonins: The machines which fold proteins. Chapter 5 in Molecular Machines. Del Lucent, Martin C. Stumpe, and Vijay Pande. ISBN 978-9814343442, World Scientific (2011).

De natura denaturantium - On the molecular basis of urea-induced protein denaturation. Martin Stumpe. Doktorarbeit (PhD Thesis). Max Planck Institute for Biophysical Chemistry & Georg-August-Universität Göttingen (2007)

Inhaltsadressiertes Auslesen in einem volumenholographischen Speichersystem mit Phasencodierung (Content-based retrieval in a volume-holographic storage system with phase-encoding). Martin Stumpe. Diplomarbeit (Diploma Thesis). Westfälische Wilhelms-Universität Münster (2003)

Patents

"Augmented reality microscope for pathology with overlay of quantitative biomarker data", WO App. WO2019199392A1

"Pathology predictions on unstained tissue", WO App. WO2019160580A1

"Focus-Weighted, Machine Learning Disease Classifier Error Prediction for Microscope Slide Images", US App. US20190340468A1

"Similar medical image search", WO App. WO2019190518A1

"Virtual staining for tissue slide images", WO App. WO2019172901A1

"Adaptive image alignment using locally optimal transformations", WO App. WO2019172890A1

"Method for creating histopathological ground truth masks using slide restaining", WO App. WO2019139591A1

"Processing fundus images using machine learning models", WO App. WO2018/035473 A3

"Augmented Reality Microscope for Pathology", WO 2018/231204 A1

"Method and system for assisting pathologist identification of tumor cells in magnified tissue images", WO App. WO2018156133A1

"Systems and Methods for Identifying Entities Directly from Imagery", US Patent App. 15/089,677

"Business change detection from street level imagery", US Patent 10,339,193 B1

"Systems and Methods for Automatically Classifying Businesses from Images", US Patent App. 14/885,452

"Business discovery from imagery", US Patent 9,594,984

(additional patent applications in filing and pending)