Michael Brudno

Publication Activity (10 Years)

Years Active: 2000-2024
Publications (10 Years): 34

Top Topics

Visual Attention

Speaker Diarization

Metric Learning

Top Venues

IEEE Trans. Vis. Comput. Graph.

Nucleic Acids Res.

Publications

Cathy Ong Ly, Balagopal Unnikrishnan, Tony Tadic, Tirth Patel, Joe Duhamel, Sonja Kandel, Yasbanoo Moayedi, Michael Brudno, Andrew Hope, Heather Ross, Chris McIntosh
Shortcut learning in medical AI hinders generalization: method for estimating AI model generalization without external data. npj Digit. Medicine 7 (1) (2024)
Alireza Hosseini, Amirhossein Kazerouni, Saeed Akhavan, Michael Brudno, Babak Taati
SUM: Saliency Unification through Mamba for Visual Attention Modeling. CoRR (2024)
Erik Christensen, Ping Luo, Andrei L. Turinsky, Mia Husic, Alaina Mahalanabis, Alaine Naidas, Juan Javier Díaz-Mejía, Michael Brudno, Trevor J. Pugh, Arun K. Ramani, Parisa Shooshtari
Evaluation of single-cell RNAseq labelling algorithms using cancer datasets. Briefings Bioinform. 24 (1) (2023)
Nicole Sultanum, Farooq Naeem, Michael Brudno, Fanny Chevalier
: Navigating large collections of text notes in electronic health records for clinical chart review. IEEE Trans. Vis. Comput. Graph. 29 (1) (2023)
Jixuan Wang, Jingbo Yang, Haochi Zhang, Helen Lu, Marta Skreta, Mia Husic, Aryan Arbabi, Nicole Sultanum, Michael Brudno
PhenoPad: Building AI enabled note-taking interfaces for patient encounters. npj Digit. Medicine 5 (2022)
Jixuan Wang, Kuan-Chieh Wang, Frank Rudzicz, Michael Brudno
Grad2Task: Improved Few-shot Text Classification Using Gradients for Task Representation. CoRR (2022)
Michael Apostolides, Yue Jiang, Mia Husic, Robert Siddaway, Cynthia Hawkins, Andrei L. Turinsky, Michael Brudno, Arun K. Ramani
MetaFusion: a high-confidence metacaller for filtering and prioritizing RNA-seq gene fusion candidates. Bioinform. 37 (19) (2021)
Jixuan Wang, Kuan-Chieh Wang, Frank Rudzicz, Michael Brudno
Grad2Task: Improved Few-shot Text Classification Using Gradients for Task Representation. NeurIPS (2021)
Jixuan Wang, Xiong Xiao, Jian Wu, Ranjani Ramamurthy, Frank Rudzicz, Michael Brudno
Speaker attribution with voice profiles by graph-based semi-supervised learning. CoRR (2021)
Jixuan Wang, Xiong Xiao, Jian Wu, Ranjani Ramamurthy, Frank Rudzicz, Michael Brudno
Speaker Attribution with Voice Profiles by Graph-Based Semi-Supervised Learning. INTERSPEECH (2020)
Pouria Mashouri, Marta Skreta, John Phillips, Dianna McAllister, Melissa Roy, Senthujan Senkaiahliyan, Michael Brudno, Devin Singh
3D Photography Based Neural Network Craniosynostosis Triaging System. ML4H@NeurIPS (2020)
Suluxan Mohanraj, J. Javier Díaz-Mejía, Martin D. Pham, Hillary Elrick, Mia Husic, Shaikh Rashid, Ping Luo, Prabnur Bal, Kevin Lu, Samarth Patel, Alaina Mahalanabis, Alaine Naidas, Erik Christensen, Danielle Croucher, Laura M. Richards, Parisa Shooshtari, Michael Brudno, Arun K. Ramani, Trevor J. Pugh
CReSCENT: CanceR Single Cell ExpressioN Toolkit. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Lauren Erdman, Marta Skreta, Mandy Rickard, Carson McLean, Aziz Mezlini, Daniel T. Keefe, Anne-Sophie Blais, Michael Brudno, Armando Lorenzo, Anna Goldenberg
Predicting Obstructive Hydronephrosis Based on Ultrasound Alone. MICCAI (3) (2020)
P. Alison Paprica, Eric Sutherland, Andrea Smith, Michael Brudno, Rosario G. Cartagena, Monique Crichlow, Brian K. Courtney, Chris Loken, Kimberlyn M. McGrail, Alex Ryan, Michael J. Schull, Adrian Thorogood, Carl Virtanen, Kathleen Yang
Essential requirements for establishing and operating data trusts: practical guidance based on a working meeting of fifteen Canadian organizations and initiatives. CoRR (2020)
Jixuan Wang, Xiong Xiao, Jian Wu, Ranjani Ramamurthy, Frank Rudzicz, Michael Brudno
Speaker diarization with session-level speaker embedding refinement using graph neural networks. CoRR (2020)
Jixuan Wang, Xiong Xiao, Jian Wu, Ranjani Ramamurthy, Frank Rudzicz, Michael Brudno
Speaker Diarization with Session-Level Speaker Embedding Refinement Using Graph Neural Networks. ICASSP (2020)
Marta Skreta, Aryan Arbabi, Jixuan Wang, Michael Brudno
Training without training data: Improving the generalizability of automated medical abbreviation disambiguation. ML4H@NeurIPS (2019)
Jixuan Wang, Kuan-Chieh Wang, Marc T. Law, Frank Rudzicz, Michael Brudno
Centroid-based Deep Metric Learning for Speaker Recognition. ICASSP (2019)
Aryan Arbabi, David R. Adams, Sanja Fidler, Michael Brudno
Identifying Clinical Terms in Free-Text Notes Using Ontology-Guided Machine Learning. RECOMB (2019)
Sebastian Köhler, Leigh Carmody, Nicole A. Vasilevsky, Julius O. B. Jacobsen, Daniel Danis, Jean-Philippe F. Gourdine, Michael A. Gargano, Nomi L. Harris, Nicolas Matentzoglu, Julie A. McMurry, David Osumi-Sutherland, Valentina Cipriani, James P. Balhoff, Tom Conlin, Hannah Blau, Gareth Baynam, Richard Palmer, Dylan Gratian, Hugh J. S. Dawkins, Michael Segal, Anna C. Jansen, Ahmed Muaz, Willie H. Chang, Jenna Bergerson, Stanley J. F. Laulederkind, Zafer Yüksel, Sergi Beltran, Alexandra F. Freeman, Panagiotis I. Sergouniotis, Daniel Durkin, Andrea L. Storm, Marc Hanauer, Michael Brudno, Susan M. Bello, Murat Sincan, Kayli Rageth, Matthew T. Wheeler, Renske Oegema, Halima Lourghi, Maria G. Della Rocca, Rachel Thompson, Francisco Castellanos, James Priest, Charlotte Cunningham-Rundles, Ayushi Hegde, Ruth C. Lovering, Catherine Hajek, Annie Olry, Luigi Notarangelo, Morgan Similuk, Xingmin Aaron Zhang, David Gómez-Andrés, Hanns Lochmüller, Hélène Dollfus, Sergio Rosenzweig, Shruti Marwaha, Ana Rath, Kathleen Sullivan, Cynthia L. Smith, Joshua D. Milner, Dorothée Leroux, Cornelius F. Boerkoel, Amy Klion, Melody C. Carter, Tudor Groza, Damian Smedley, Melissa A. Haendel, Chris Mungall, Peter N. Robinson
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. 47 (Database-Issue) (2019)
Nicole Sultanum, Devin Singh, Michael Brudno, Fanny Chevalier
Doccurate: A Curation-Based Approach for Clinical Text Visualization. IEEE Trans. Vis. Comput. Graph. 25 (1) (2019)
Jixuan Wang, Kuan-Chieh Wang, Marc T. Law, Frank Rudzicz, Michael Brudno
Centroid-based deep metric learning for speaker recognition. CoRR (2019)
Marta Skreta, Aryan Arbabi, Jixuan Wang, Michael Brudno
Training without training data: Improving the generalizability of automated medical abbreviation disambiguation. CoRR (2019)
Sana Tonekaboni, Mjaye Mazwi, Peter Laussen, Danny Eytan, Robert Greer, Sebastian D. Goodfellow, Andrew J. Goodwin, Michael Brudno, Anna Goldenberg
Prediction of Cardiac Arrest from Physiological Signals in the Pediatric ICU. MLHC (2018)
Michael Glueck, Mahdi Pakdaman Naeini, Finale Doshi-Velez, Fanny Chevalier, Azam Khan, Daniel Wigdor, Michael Brudno
PhenoLines: Phenotype Comparison Visualizations for Disease Subtyping via Topic Models. IEEE Trans. Vis. Comput. Graph. 24 (1) (2018)
Nicole Sultanum, Michael Brudno, Daniel Wigdor, Fanny Chevalier
More Text Please! Understanding and Supporting the Use of Visualization for Clinical Text Overview. CHI (2018)
Zhihao Luo, Marcus A. Brubaker, Michael Brudno
Size and Texture-Based Classification of Lung Tumors with 3D CNNs. WACV (2017)
Zihan Wang, Michael Brudno, Orion J. Buske
Towards a Directory of Rare Disease Specialists: Identifying Experts from Publication History. MLHC (2017)
Michael Glueck, Alina Gvozdik, Fanny Chevalier, Azam Khan, Michael Brudno, Daniel Wigdor
PhenoStacks: Cross-Sectional Cohort Phenotype Comparison Visualizations. IEEE Trans. Vis. Comput. Graph. 23 (1) (2017)
Sebastian Köhler, Nicole A. Vasilevsky, Mark Engelstad, Erin Foster, Julie A. McMurry, Ségolène Aymé, Gareth Baynam, Susan M. Bello, Cornelius F. Boerkoel, Kym M. Boycott, Michael Brudno, Orion J. Buske, Patrick F. Chinnery, Valentina Cipriani, Laureen E. Connell, Hugh J. S. Dawkins, Laura E. DeMare, Andrew Devereau, Bert B. A. de Vries, Helen V. Firth, Kathleen Freson, Daniel Greene, Ada Hamosh, Ingo Helbig, Courtney Hum, Johanna Jähn, Roger James, Roland Krause, Stanley J. F. Laulederkind, Hanns Lochmüller, Gholson J. Lyon, Soichi Ogishima, Annie Olry, Willem H. Ouwehand, Nikolas Pontikos, Ana Rath, Franz Schaefer, Richard H. Scott, Michael Segal, Panagiotis I. Sergouniotis, Richard Sever, Cynthia L. Smith, Volker Straub, Rachel Thompson, Catherine Turner, Ernest Turro, Marijcke W. M. Veltman, Tom Vulliamy, Jing Yu, Julie von Ziegenweidt, Andreas Zankl, Stephan Züchner, Tomasz Zemojtel, Julius O. B. Jacobsen, Tudor Groza, Damian Smedley, Christopher J. Mungall, Melissa A. Haendel, Peter N. Robinson
The Human Phenotype Ontology in 2017. Nucleic Acids Res. 45 (Database-Issue) (2017)
Bo Liu, Hongzhe Guo, Michael Brudno, Yadong Wang
deBGA: read alignment with de Bruijn graph-based seed and extension. Bioinform. 32 (21) (2016)
Michael Glueck, Peter Hamilton, Fanny Chevalier, Simon Breslav, Azam Khan, Daniel J. Wigdor, Michael Brudno
PhenoBlocks: Phenotype Comparison Visualizations. IEEE Trans. Vis. Comput. Graph. 22 (1) (2016)
Yael Kamil, Kym M. Boycott, Daniel Gross, Marta Gîrdea, Sergiu Dumitriu, Michael Brudno
Integrating Rare Disease Research Patient Workflows and Deep Phenotyping into the Epic© EMR. CRI (2016)
Aryan Arbabi, Ladislav Rampásek, Michael Brudno
Cell-free DNA fragment-size distribution analysis for non-invasive prenatal CNV prediction. Bioinform. 32 (11) (2016)
Orion J. Buske, AshokKumar Manickaraj, Seema Mital, Peter N. Ray, Michael Brudno
Identification of deleterious synonymous variants in human genomes. Bioinform. 31 (5) (2015)
Ladislav Rampásek, Aryan Arbabi, Michael Brudno
Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing. Bioinform. 30 (12) (2014)
Alexander Poliakov, Justin Foong, Michael Brudno, Inna Dubchak
GenomeVISTA - an integrated software package for whole-genome alignment and visualization. Bioinform. 30 (18) (2014)
Sebastian Köhler, Sandra C. Doelken, Christopher J. Mungall, Sebastian Bauer, Helen V. Firth, Isabelle Bailleul-Forestier, Graeme C. M. Black, Danielle L. Brown, Michael Brudno, Jennifer Campbell, David R. FitzPatrick, Janan T. Eppig, Andrew P. Jackson, Kathleen Freson, Marta Gîrdea, Ingo Helbig, Jane A. Hurst, Johanna Jähn, Laird G. Jackson, Anne M. Kelly, David H. Ledbetter, Sahar Mansour, Christa L. Martin, Celia Moss, Andrew D. Mumford, Willem H. Ouwehand, Soo-Mi Park, Erin Rooney Riggs, Richard H. Scott, Sanjay Sisodiya, Steven Van Vooren, Ronald J. Wapner, Andrew O. M. Wilkie, Caroline F. Wright, Anneke T. Vulto-van Silfhout, Nicole de Leeuw, Bert B. A. de Vries, Nicole L. Washington, Cynthia L. Smith, Monte Westerfield, Paul N. Schofield, Barbara J. Ruef, Georgios V. Gkoutos, Melissa A. Haendel, Damian Smedley, Suzanna E. Lewis, Peter N. Robinson
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 42 (Database-Issue) (2014)
Orion J. Buske, AshokKumar Manickaraj, Seema Mital, Peter N. Ray, Michael Brudno
Identification of deleterious synonymous variants in human genomes. Bioinform. 29 (15) (2013)
Nilgun Donmez, Michael Brudno
SCARPA: scaffolding reads with practical algorithms. Bioinform. 29 (4) (2013)
Marc Fiume, Eric J. M. Smith, Andrew Brook, Dario Strbenac, Brian Turner, Aziz M. Mezlini, Mark D. Robinson, Shoshana J. Wodak, Michael Brudno
Savant Genome Browser 2: visualization and analysis for population-scale genomics. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
David Warde-Farley, Michael Brudno, Quaid Morris, Anna Goldenberg
Mixture Model for Sub-Phenotyping in GWAS. Pacific Symposium on Biocomputing (2012)
Yue Jiang, Yadong Wang, Michael Brudno
PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants. Bioinform. 28 (20) (2012)
Joseph Andrew Whitney, Judice L. Y. Koh, Michael Costanzo, Grant Brown, Charles Boone, Michael Brudno
Clustering with Overlap for Genetic Interaction Networks via Local Search Optimization. WABI (2011)
H. Andrés Lagar-Cavilla, Joseph Andrew Whitney, Roy Bryant, Philip Patchin, Michael Brudno, Eyal de Lara, Stephen M. Rumble, Mahadev Satyanarayanan, Adin Scannell
SnowFlock: Virtual Machine Cloning as a First-Class Cloud Primitive. ACM Trans. Comput. Syst. 29 (1) (2011)
Orion J. Buske, Misko Dzamba, Justin Foong, Lynette Lau, Marc Fiume, Christian Marshall, Susan Walker, Aparna Prasad, Michael Brudno
Variant detection and the Autism sequencing project. BMC Bioinform. 12 (S-11) (2011)
Matei David, Misko Dzamba, Dan Lister, Lucian Ilie, Michael Brudno
SHRiMP2: Sensitive yet Practical Short Read Mapping. Bioinform. 27 (7) (2011)
Nilgun Donmez, Michael Brudno
Hapsembler: An Assembler for Highly Polymorphic Genomes. RECOMB (2011)
Can Alkan, Michael Brudno, Evan E. Eichler, Maricel G. Kann, Süleyman Cenk Sahinalp
Session Introduction. Pacific Symposium on Biocomputing (2010)
Seunghak Lee, Eric P. Xing, Michael Brudno
MoGUL: Detecting Common Insertions and Deletions in a Population. RECOMB (2010)
Adrian V. Dalca, Stephen M. Rumble, Samuel Levy, Michael Brudno
VARiD: A variation detection framework for color-space and letter-space platforms. Bioinform. 26 (12) (2010)
Adrian V. Dalca, Michael Brudno
Genome variation discovery with high-throughput sequencing data. Briefings Bioinform. 11 (1) (2010)
Marc Fiume, Vanessa Williams, Andrew Brook, Michael Brudno
Savant: genome browser for high-throughput sequencing data. Bioinform. 26 (16) (2010)
Paul Medvedev, Michael Brudno
Maximum Likelihood Genome Assembly. J. Comput. Biol. 16 (8) (2009)
Philip Patchin, H. Andrés Lagar-Cavilla, Eyal de Lara, Michael Brudno
Adding the easy button to the cloud with SnowFlock and MPI. HPCVirt@EuroSys (2009)
Michael Brudno, Paul Medvedev, Jens Stoye, Francisco M. de la Vega
A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG). Bioinform. 25 (21) (2009)
Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Arend Sidow, Michael Brudno
SHRiMP: Accurate Mapping of Short Color-space Reads. PLoS Comput. Biol. 5 (5) (2009)
Horacio Andrés Lagar-Cavilla, Joseph Andrew Whitney, Adin Matthew Scannell, Philip Patchin, Stephen M. Rumble, Eyal de Lara, Michael Brudno, Mahadev Satyanarayanan
SnowFlock: rapid virtual machine cloning for cloud computing. EuroSys (2009)
Michael Brudno, Bernard M. E. Moret, C. Randal Linder, Tandy J. Warnow
Session Introduction. Pacific Symposium on Biocomputing (2008)
Paul Medvedev, Michael Brudno
Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads. RECOMB (2008)
Adrian V. Dalca, Michael Brudno
FRESCO: Flexible Alignment with Rectangle Scoring Schemes. Pacific Symposium on Biocomputing (2008)
Gerald T. Quon, Yee Whye Teh, Esther T. Chan, Timothy R. Hughes, Michael Brudno, Quaid Morris
A mixture model for the evolution of gene expression in non-homogeneous datasets. NIPS (2008)
Seunghak Lee, Elango Cheran, Michael Brudno
A robust framework for detecting structural variations in a genome. ISMB (2008)
Vladimir Yanovski, Stephen M. Rumble, Michael Brudno
Read Mapping Algorithms for Single Molecule Sequencing Data. WABI (2008)
Paul Medvedev, Konstantinos Georgiou, Gene Myers, Michael Brudno
Computability of Models for Sequence Assembly. WABI (2007)
Michael Brudno, Alexander Poliakov, Simon Minovitsky, Igor Ratnere, Inna Dubchak
Multiple whole genome alignments and novel biomedical applications at the VISTA portal. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Galina Yu. Kovaleva, Georgii A. Bazykin, Michael Brudno, Mikhail S. Gelfand
Comparative Genomics of Transcriptional Regulation in Yeasts and its Application to Identification of a Candidate Alpha-isopropylmalate Transporter. J. Bioinform. Comput. Biol. 4 (5) (2006)
Nameeta Y. Shah, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, E. Wes Bethel, Edward M. Rubin, Bernd Hamann, Inna Dubchak
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinform. 20 (5) (2004)
Chuong B. Do, Michael Brudno, Serafim Batzoglou
PROBCONS: Probabilistic Consistency-Based Multiple Alignment of Amino Acid Sequences. AAAI (2004)
Michael Brudno, Rasmus Steinkamp, Burkhard Morgenstern
The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Mukund Sundararajan, Michael Brudno, Kerrin S. Small, Arend Sidow, Serafim Batzoglou
Chaining Algorithms for Alignment of Draft Sequence. WABI (2004)
Leila Taher, Oliver Rinner, Saurabh Garg, Alexander Sczyrba, Michael Brudno, Serafim Batzoglou, Burkhard Morgenstern
AGenDA: homology-based gene prediction. Bioinform. 19 (12) (2003)
Michael Brudno, Sanket Malde, Alexander Poliakov, Chuong B. Do, Olivier Couronne, Inna Dubchak, Serafim Batzoglou
Glocal alignment: finding rearrangements during alignment. ISMB (Supplement of Bioinformatics) (2003)
Michael Brudno, Michael Chapman, Berthold Göttgens, Serafim Batzoglou, Burkhard Morgenstern
Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinform. 4 (2003)
Michael Brudno, Burkhard Morgenstern
Fast and Sensitive Alignment of Large Genomic Sequences. CSB (2002)
Chris Mayor, Michael Brudno, Jody R. Schwartz, Alexander Poliakov, Edward M. Rubin, Kelly A. Frazer, Lior Pachter, Inna Dubchak
VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinform. 16 (11) (2000)
I. Dralyuk, Michael Brudno, Mikhail S. Gelfand, Manfred Zorn, Inna Dubchak
ASDB: database of alternatively spliced genes. Nucleic Acids Res. 28 (1) (2000)