- Alex Chang, Vinith M. Suriyakumar, Abhishek Moturu, Nipaporn Tewattanarat, Andrea Doria, Anna Goldenberg (2020). Using Generative Models for Pediatric wbMRI. arXiv preprint arXiv:2006.00727
- Chun-Hao Chang, Sarah Tan, Ben Lengerich, Anna Goldenberg, Rich Caruana (2020). How Interpretable and Trustworthy are GAMs? arXiv preprint arXiv:2006.06466
- Matthew B.A. McDermott, Bret Nestor, Evan Kim, Wancong Zhang, Anna Goldenberg, Peter Szolovits, Marzyeh Ghassemi
(2020). A Comprehensive Evaluation of Multi-task Learning and Multi-task Pre-training on EHR Time-series Data. arXiv preprint arXiv:2007.10185
- Vinith M. Suriyakumar, Nicolas Papernot, Anna Goldenberg, Marzyeh Ghassemi(2020).Chasing Your Long Tails: Differentially Private Prediction in Health Care Settings. arXiv preprint arXiv:2010.06667
- Erik Drysdale, Devin Singh, Anna Goldenberg (2020).Forecasting Emergency Department Capacity Constraints for COVID Isolation Beds. arXiv preprint arXiv:2011.06058
- S Tonekaboni, S Joshi, D Duvenaud, A Goldenberg (2020). What went wrong and when? Instance-wise Feature Importance for Time-series Models. arXiv preprint arXiv:2003.02821
- AM Mezlini, S Das, A Goldenberg (2020) Finding associations in a heterogeneous setting: Statistical test for aberration enrichment. BioRxiv
- Zitnik M, Nguyen F, Wang B, Leskovec J, Goldenberg A, Hoffman MM. Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities. Inf Fusion. 2019;50: 71–91
- CH Chang, L Rampasek, A Goldenberg Dropout Feature Ranking for Deep Learning Models:
arXiv preprint arXiv:1712.08645.
- Adam GA, Smirnov P, Duvenaud D, Haibe-Kains B, Goldenberg A. Stochastic Combinatorial Ensembles for Defending Against Adversarial Examples. 2018.
- Chang C-H, Creager E, Goldenberg A, Duvenaud D. Explaining Image Classifiers by Counterfactual Generation. 2018.
- Ng B, Jafarzadeh S, Cole D, Goldenberg A, Mostafavi S. DNA Methylation Network Estimation with Sparse Latent Gaussian Graphical Model 2018.
- L Rampasek, A Goldenberg: Dr. VAE: Drug Response Variational Autoencoder:
arXiv preprint arXiv:1706.08203.
- Melissa D McCradden, Shalmali Joshi, James A Anderson, Mjaye Mazwi, Anna Goldenberg, Randi Zlotnik Shaul. (2020)Patient safety and quality improvement: Ethical principles for a regulatory approach to bias in healthcare machine learning
- Maria J. Aristizabal, Ina Anreiter, Thorhildur Halldorsdottir, Candice L. Odgers, Thomas W. McDade, Anna Goldenberg, Sara Mostafavi, Michael S. Kobor, Elisabeth B. Binder, Marla B. Sokolowski, and Kieran J. O’Donnell. (2020)Biological embedding of experience: A primer on epigenetics
- Lauren Erdman, Marta Skreta, Mandy Rickard, Carson McLean, Aziz Mezlini, Daniel T. Keefe, Anne-Sophie Blais, Michael Brudno, Armando Lorenzo, Anna Goldenberg (2020). Predicting Obstructive Hydronephrosis Based on Ultrasound Alone
- Angeline Yasodhara, Victor Dong, Amirhossein Azhie,Anna Goldenberg, Mamatha Bhat. (2020) Identifying Modifiable Predictors of Long‐term Survival in Liver Transplant Recipients with Diabetes using Machine Learning
- GA Adam, L Rampášek, Z Safikhani, P Smirnov, B Haibe-Kains, A Goldenberg. (2020) Machine Learning Approaches to Drug Response Prediction: Challenges and Recent Progress. Nature Precision Oncology
- MD McCradden, S Joshi, JA Anderson, M Mazwi, A Goldenberg, R Zlotnik Shaul. (2020). Patient safety and quality improvement: Ethical principles for a regulatory approach to bias in healthcare machine learning. Journal of the American Medical Informatics Association.
- Z Liu, QP Nguyen, Q Guan, A Albulescu, L Erdman, Y Mahdaviyeh, J Kang, H Ouyang, RG Hegele, T Moraes, A Goldenberg, SD Dell, V Mennella. (2020) A quantitative super-resolution imaging toolbox for diagnosis of motile ciliopathies. Science Translational Medicine 12(535)
- SWM Eng, JM Olazagasti, A Goldenberg, CS Crowson, CV Oddis, TB Niewold, RSM Yeung, AM Reed (2020) A Clinically and Biologically Based Subclassification of the Idiopathic Inflammatory Myopathies Using Machine Learning. ACR Open Rheumatology. doi: 10.1002/acr2.11115
- A Spann, A Yasodhara, J Kang, K Watt, B Wang, A Goldenberg, M Bhat. (2020) Applying Machine Learning in Liver Disease amd Transplantation: A Comprehensive Review. Hepatology. doi:10.1002/hep.31103
- MJ. Aristizabal, I Anreiter, T Halldorsdottir, CL. Odgers, TW. McDade, A Goldenberg, S Mostafavi, MS. Kobor, EB. Binder, MB. Sokolowski, KJ. O’Donnell (2019). Biological Embedding of Experience: a primer on epigenetics, PNAS. https://doi.org/10.1073/pnas.1820838116
- J Wiens, S Saria, M Sendak, M Ghassemi, VX Liu, F Doshi-Velez, K Jung, K Heller, D Kale, M Saeed, PN Ossorio, S Thadaney-Israni, A Goldenberg. (2019). Do no harm: a roadmap for responsible machine learning for health care. Nature Medicine. doi: 10.1038/s41591-019-0548-6
- H Suzuki, SA Kumar, S Shuai, A Diaz-Navarro, …, A Goldenberg, ... , JA Calarco, L Stein, MD Taylor. (2019) Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma. Nature, v 574, i 7780, pp 707-711
- MP Menden, D Wang, MJ Mason, B Szalai, KC Bulusu, ..., AstraZeneca-Sanger Drug Combination DREAM Consortium, ..., S Fawell, G Stolovitzky, J Guinney, JR Dry , J Saez-Rodriguez. (2019) Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications.
- AS Mer, W Ba-Alawi, P Smirnov, YX Wang, B Brew, J Ortmann, MS Tsao, DW Cescon, A Goldenberg, Haibe-Kains B. (2019) Integrative Pharmacogenomics Analysis of Patient-Derived Xenografts. Cancer Research. doi: 10.1158/0008-5472.CAN-19-034
- A Oyefiade A, L Erdman, A Goldenberg, D Malkin, E Bouffet, MD Taylor, V Ramaswamy, N Scantlebury, N Law, DJ Mabbott. (2019) PPAR and GST polymorphisms may predict changes in intellectual functioning in medulloblastoma survivors. Journal of Neurooncology. 142(1):39-48
- W Nelson, M Zitnik, B Wang, J Leskovec, A Goldenberg*, R Sharan*. (2019) To embed or not: network embedding as a paradigm in computational biology. Frontiers in Genetics, section Systems Biology. 1;10:381
- L. Rampasek, D. Hidru, P. Smirnov, B. Haibe-Kains, A. Goldenberg. (2019). Dr. VAE: Improving drug response prediction via modeling of drug perturbation effects. Bioinformatics. Oxford University Press. btz158, https://doi.org/10.1093/bioinformatics/btz158
- M Zitnik, F Nguyen, B Wang, J Leskovec, A Goldenberg, MM Hoffman (2019) Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities. Information Fusion. 50, 71-91
- ASingh Mer, W Ba-Alawi, P Smirnov, YX Wang, B Brew, MS Tsao, D Cescon, A Goldenberg, Benjamin Haibe-Kains. (2019) Systematic pharmacogenomic analysis of large patient derived xenografts data.
- Victor JC, Charles Victor J, Alison Paprica P, Brudno M, Virtanen C, Wodchis W, et al. The Ontario Data Safe Haven: Bringing High Performance Computing to Population-wide Data Assets. International Journal of Population Data Science. 2018;3. doi:10.23889/ijpds.v3i4.753
- S Shen, R Singhania, G Fehringer, A Chakravarthy, MHA Roehrl, ..., Anna Goldenberg, Trevor J. Pugh, Michael M. Hoffman, Scott V. Bratman, Rayjean J. Hung & Daniel D. De Carvalho (2018) Sensitive tumour detection and classification using plasma cell-free DNA methylomes. Nature 563 pp. 579-583
- de Vega WC, Erdman L, Vernon SD, Goldenberg A, McGowan PO. Integration of DNA methylation & health scores identifies subtypes in myalgic encephalomyelitis/chronic fatigue syndrome. Epigenomics. 2018;10: 539–557
- Tonekaboni S, Mazwi M, Laussen PC, Eytan D, Goldenberg A. Prediction of Cardiac Arrest from Physiological Signals in the Pediatric ICU. Proceedings of Machine Learning for Healthcare 2018
- L. Rampasek, A. Goldenberg. Learning from the everyday images enables expert-like diagnosis of retinal diseases. Cell
- Andréanne N. Zizzo, Andréanne N. Zizzo, Andréanne N. Zizzo, Lauren Erdman, MSc, Brian M. Feldman, MD, MSc, FRCPC, Anna Goldenberg, PhD
(2018) Similarity Newtword Fusion: A Novel Application to Making Clinical Diagnoses. Rheumatic Disease Clinics
- W. Vega, L. Erdman, S. Vernon, A. Goldenberg, P. McGowan, Integration of DNA methylation and health scores identifies subtypes in myalgic encephalomyelitis/chronic fatigue syndrome. Future Medicine.
- L. Stefalnik, L. Erdman, S.H. Ameis, G. Foussias, B. Mulsant, T. Behdinan, A. Goldenberg, L.J. O’Donnell, A.N. Voineskos (2017) Brain-Behavior Participant Similarity Networks Among Youth and Emerging Adults with Schizophrenia Spectrum, Autism Spectrum, or Bipolar Disorder and Matched Controls. Neuropsychopharmacology.
- C. Azencott, DREAM Idea Challenge Consortium, T. Norman, S. Friend, G. Stolovitzky, A. Goldenberg (2017) The inconvenience of data of convenience: computational research beyond post-mortem analyses. Nature Methods, 14, pp. 937–938.
- Y. Mamatjan, S. Agnihotri, A. Goldenberg, P. Tonge, G. Zadeh, K. Aldape. (2017) Molecular signatures for tumor classification: an analysis of TCGA data. Journal of Molecular Diagnostics. In Press.
- A. Mezlini, A. Goldenberg (2017) Incorporating Networks in a Probabilistic Graphical Model to Find Drivers for Complex Human Diseases. PloS Computational Biology, Oct 12;13(10):e1005580.
- B. Wang, L. Huang, Y. Zhu, A. Kundaje, S. Batzoglou, A. Goldenberg (2017) Vicus: Exploiting Local Structures to Improve Biological Network Analysis. PloS Computational Biology, Oct 12;13(10):e1005621
- H. Hou, L. Uuskula-Reimand, M. Makarem, S. Saleh, C. Corre, A. Metcalf, A. Goldenberg*, M. Palmert*, M. Wilson* (2017) Gene expression profiling of puberty-associated genes reveals abundant itssue and sex-specific changes across postnatal development. Human Molecular Genetics. Sep 15;26(18):3585-3599
- TCGA Consortium (2017). Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. Cancer Cell, 32(2), pp.185-203
- F.MG. Cavalli, M. Remke, L. Rampasek, D.JH Shih, ..., A.Goldenberg*, V. Ramaswamy*, M.D. Taylor* (2017) Intertumoral heterogeneity within medulloblastoma subgroups. Cancer Cell, 31(6): 737-754
- M. Leung, D. G. Bassani, A. Racine-Poon, A. Goldenberg, S. A. Ali, Gagandeep Kang, P. S. Premkumar and D E. Roth. (2017) Conditional Random Slope: A new approach for estimating individual child growth velocity in epidemiological research. American Journal of Human Biology, accepted. DOI: 10.1002/ajhb.23009
- N. El-Hachem, D.Gendoo, L.Ghoraie, Z.Safikhani, P.Smirnov, C.Chung, K.Deng, A.Fang, E.Birkwood, C.Ho, R.Isserlin, G.Bader, A.Goldenberg, and B.Haibe-Kains (2017). Integrative cancer pharmacogenomics to infer large-scale drug taxonomy. Cancer Research, 77(11):3057-3069
- Z. Safikhani, N. El-Hachem, P. Smirnov, M. Freeman, A. Goldenberg, N.J. Birkbak, A.H. Beck, H.J.W.L. Aerts, J. Quackenbush and B. Haibe-Kains (2016). Safikhani et al. reply. Nature, 540, E2–E4
- Z. Safikhani, N. El Hachem, R. Quevedo, P. Smirnov, A. Goldenberg, N.J. Birkbak, C. Mason, C. Hatzis, L. Shi, H.J. Aerts, J. Quackenbush and B. Haibe-Kains. (2016) Assessment of pharmacogenomic agreement. F1000Research, 5, pp 825
- SK Sieberts, F Zhu, J Garcia, E Stahl, A. Pratap, G. Pandey, D. Pappas, D. Aguilar, B. Anton, J. Bonet, R. Eksi, O. Fornes, E. Guney, G. Li, M.A Marin, B. Panwar, J. PlanasIglesias, D. Poglayen, J. Cui, AO. Flcao, C. Suver, B. Hoff, VSK. Blagurusamy, D. Dillenberger, EC. Neto, T. Norman, T. Aittokallio, M. Ammad-ud-din, C. Azencott, V. Bellon, V. Boeva, K. Bunte…, A. Goldenberg,…, M Hajiloo, D. Hidru, …, B. Wang, …, L. Mangravite(2016) Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nature Communications, 7(1), p. 12460
- P Smirnov, Z Safikhani, N El-Hachem, D Wang, A She, C Olsen, M Freeman, H Selby, D Gendoo, P Grossman, A Beck, H Aerts, M Lupien, A Goldenberg, B Haibe-Kains. (2015) PharmacoGx: an R package for analysis of large pharmacogenomics datasets. In submission to Bioinformatics.
- C Corre, G Shinoda, H Zhu, DL Cousminer, C Crossman, C Bellissimo, A Goldenberg, GQ Daley, MR Palmart. (2015) Sex specific regulation of weight and puberty by Lin28/let-7 axis. In submission to the Journal of Endocrinology.
- R. Colak, T. Kim, H Kazan, Y Oh, M Cruz, A Valladares, J Peralta, J Escobedo, E Parra, P.M. Kim and A. Goldenberg (2015) JBASE: Joint Bayesian Analysis of Sub-phenotypes and Epistasis. Bioinformatics.
- Saria, S., A. Goldenberg (2015). Subtyping: What it is and its role in precision medicine. IEEE Intelligent Systems Magazine. 30(4). pp 70-75.
D Hidru and A Goldenberg (2014) EquiNMF: Graph Regularized Multiview Nonnegative Matrix Factorization. Workshop on Machine Learning in Computational Biology co-located with NIPS.
- A.M. Mezlini, C. Baciu, S. Morrissy, M. Taylor, D. Malkin, A. Goldenberg (2014) Quantity or quality that is the question: integrative genome-wide association. In Proceedings of the ASHG Conference.
- B Wang, A Mezlini, F Demir, M Fiume, T Zu, M Brudno, B Haibe-Kains and A Goldenberg (2014) Similarity network fusion for aggregating data types on a genomic scale. Nature Methods. Online Jan 26.
- A Mezlini, B Wang, A Deshwar, Q Morris and A Goldenberg (2013) Identifying cancer specific functionally relevant miRNAs from gene expression and miRNA-to-gene networks using regularized regression. PloS One, 8(10).
- Y Li, A Goldenberg, K Wong, Z Zhang (2013) A probabilistic approach to explore human microRNA targetome by integrating microRNA-overexpression data and sequence information. Bioinformatics.
- A M Mezlini, E JM Smith, M Fiume, O Buske, G Savich, S Shah, S Aparicion, D Chiang, A Goldenberg and M Brudno (2013) iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Research.
- B Wang and A Goldenberg (2012) Local Diffusion and Cluster Score (LDCS) for Disease Subtyping. Electronic proceeds of the workshop on Machine Learning in Computational Biology, collocated w/ NIPS.
- Mostafavi S, Goldenberg A, Morris Q (2012) Labeling Nodes Using Three Degrees of Propagation. PLoS ONE 7(12): e51947. doi:10.1371/journal.pone.0051947.
- M.Alshalalfa, G. Bader, A. Goldenberg, Q. Morris, R. Alhajj (2012) Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. BMC Systems Biology 6(1): 112.
- B.Wang, A. Mezlini and A. Goldenberg (2012) Combining multiple biological domains using patient network fusion. In Proceedings of the Machine Learning in Genetics and Genomics Workshop co-located with ICML.
- D.Warde-Farley, M. Brudno, Q. Morris, A Goldenberg (2012) Sub-phenotype Modeling in GWAS. In Proceedings of the Pacific Symposium on Biocomputing.
- A Goldenberg, S Mostafavi, G Quon, P Boutros, and Q Morris. (2011) Unsupervised detection of genes of influence in lung cancer using biological networks. Bioinformatics.
- A Goldenberg and A Zheng (2006) Exploratory Study of a New Model for Evolving Networks, Lecture Notes in Computer Science, Vol 4503.
- A Goldenberg, D Warde-Farley, M. Brudno, Q. Morris (2010) Mixture model for sub-phenotyping. Electronic proceedings of the workshop on Machine Learning in Computational Biology, collocated with NIPS.
- S Mostafavi, A Goldenberg, and Q Morris. (2010) Predicting Node Labels in Large Networks. Electronic Proceedings of the Workshop on Networks Across Disciplines: Theory and Applications.
- S Mostafavi, A Goldenberg and Q Morris. (2010) Predicting Node Characteristics from Molecular Networks. Chapter in Network Biology: Methods and Protocols, Springer.
- A Goldenberg, A Zheng, S Fienberg and E Airoldi (2009) A Survey of Statistical Network Models, Foundations and Trends in Machine Learning, Vol 2 (2): pp 129-233.
- A Goldenberg (2007) Scalable Graphical Models for Social Networks. PhD Thesis.
- A Goldenberg and A Zheng (2006) Exploratory Study of a New Model for Evolving Networks,
Lecture Notes in Computer Science, Vol 4503.
- A Goldenberg and A Moore (2005) Bayes Net Graphs to Understand Coauthorship Networks, KDD Workshop on Link Discovery: Issues, Approaches and Applications.
- A Goldenberg and A Moore (2004) Tractable Learning of Large Bayes Net Structures from Sparse
Data, Proceedings of the Twenty First International Conference on Machine Learning.
- A Goldenberg, J Kubica, P Komarek, A Moore and J Schneider (2003) A Comparison of Statistical and Machine Learning Algorithms on the Task of Link Completion, KDD Workshop on Link Analysis for Detecting Complex Behavior.
- A Goldenberg and A Moore (2003) Empirical Bayes Screening for Link Analysis, Workshop on Text
Analysis and Link Detection, International Joint Conference on Artificial Intelligence
- A Goldenberg, G Shmueli, R Caruana and S Fienberg (2002) Early statistical detection of anthrax
outbreaks by tracking over-the-counter medication sales, PNAS, 99, 5237 - 5240.
- P Yu, A Goldenberg and Z Bi (2001) Time Series Forecasting Using Wavelets with Predictor-Corrector Boundary Treatment, KDD Workshop on Temporal Data Mining.
- M Kantardzic, A Goldenberg, T Howe and P Fagey (2001) Artificial Neural Network Approach to Data Analysis and Parameter Estimation in Experimental Spectroscopy, Informatica, Vol 25, 1926.
- David Malkin, Nicholas Light, Valli Subrasi, Benjamin Brew, Sangeetha Paramathas, Arash Nabbi, Sergei Prykhozhij, Trevor Pugh, Jason Berman, Anna Goldenberg, Adam Shlien (2020). Abstract IA02: Novel strategies for early cancer detection and prevention: The Li-Fraumeni syndrome story.
- George Alexandru Adam, Chun-Hao Kingsley Chang, Benjamin Haibe-Kains, Anna Goldenberg ; Proceedings of the 5th Machine Learning for Healthcare Conference, PMLR 126:710-731, 2020. Hidden Risks of Machine Learning Applied to Healthcare: Unintended Feedback Loops Between Models and Future Data Causing Model Degradation.
- Bret Nestor, Liam G. McCoy, Amol Verma, Chloe Pou-Prom, Joshua Murray, Sebnem Kuzulugil, David Dai, Muhammad Mamdani, Anna Goldenberg, Marzyeh Ghassemi;Proceedings of the 5th Machine Learning for Healthcare Conference, PMLR 126:950-972, 2020. Preparing a Clinical Support Model for Silent Mode in General Internal Medicine.
- ASingh Mer, W Ba-Alawi, P Smirnov, YX Wang, B Brew, MS Tsao, D Cescon, A Goldenberg, Benjamin Haibe-Kains. (2019) Systematic pharmacogenomic analysis of large patient derived xenografts data.
- A.Goldenberg and B. Wang. Optimizing risk stratification to discover novel neuroblastoma genes,
American Society for Human Genetics (ASHG), San Francisco, 2012
- B.Wang, A. Mezlini and A. Goldenberg. Combining multiple biological domains using patient
network fusion. Oral Presentation. International Conference on Systems Biology (ICSB), Toronto,2012
- R.Colak, H., Kazan, A. Hussin, Y. Oh, P.M. Kim, A. Goldenberg JBASE: Joint Bayesian Analyis of
Sub-phenotypes and Epistasis, Poster, Genome Informatics, Cold Spring Harbour, NY, USA, 2011
- A.Goldenberg, S. Mostafavi, G. Quon, A. Deshwar, P.C, Boutros and Q. Morris. Identifying
miRNAs regulatory networks using mRNA expression data, Oral presentation, Systems Biology:
Networks, Cold Spring Harbour, NY 2011
- A.Goldenberg, S. Mostafavi, G. Quon, P.C. Boutros and Q. Morris. Identifying genes important at
the onset of lung cancer, Poster, AACR-NCI Conference on Systems Biology: Confronting the
Complexity of Cancer, San Diego, 2011
- D.Foster, A. Goldenberg, L. Ungar Maximal Subset Feature Selection for BioInformatics Ungar
Snowbird Learning Workshop, 2008