Publications
Publications
Pre-prints
Featured
Xu, Witten, and Shojaie (2025) A unified framework for semi-parametrically efficient semi-supervised learning. arXiv:2502.17741
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2024
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Kong, Ancell, Witten, and Zweifel (2024) Valence and salience encoding in the central amygdala. eLife 13: RP101980.
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2023
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Tan, Sun, and Witten (2023) Sparse reduced rank Huber regression in high dimensions. Journal of the American Statistical Association 118(544): 2383–2393.
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2022
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Yu, Witten, and Bien (2022) Controlling costs: feature selection on a budget. STAT 11(1): e427.
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2021
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Fleming, Jewell, Engelhard, Witten, and Witten (2021) Inferring spikes from calcium imaging in dopamine neurons. PLoS ONE 16(6): e0252345.
Nofallah, Mehta, Mercan, . . . and Shapiro. (2021) Machine learning techniques for mitoses classification. Computerized Medical Imaging and Graphics 87: 101832.
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Zhao, Witten, and Shojaie (2021) In defense of the indefensible: a very naive approach to high-dimensional inference. Statistical Science 36(4): 562-577.
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2020
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Xia, Ma, Cui, Bzdok, Thirion, Bassett, Satterthwaite, Shinohara, Witten (2020) Multi-Scale Network Regression .... Human Brain Mapping 41: 2553-2566.
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Shen, Gao, Witten, and Han (2020) Optimal estimation of variance in non-parametric regression with random design. Annals of Statistics 48(6): 3589-3618.
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Shen, Han, and Witten (2020) Exponential inequalities for dependent V-statistics via random Fourier features. Electronic Journal of Probability 25(7): 1-18.
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de Vries, Lecoq, Buice, . . . , Witten, . . . and Koch (2020) A large-scale, standardized physiological survey reveals higher order... Nature Neuroscience 23: 138-151.
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Padilla, Sharpnack, Chen, and Witten (2020) Adaptive non-parametric regression with the K-NN fused lasso. Biometrika 107(2): 293-310.
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2019
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Zdeblick, Shea-Brown, Witten, and Buice (2019). Data-driven discovery of functional cell types that improve models of neural activity. NeurIPS Neuro-AI Workshop.
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Yu, Bien, and Witten (2019) Discussion of “Covariate-assisted ranking and screening for large-scale ...” Journal of the Royal Statistical Society, Series B 81(2): 229-231.
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Jewell and Witten (2019) Discussion of “Gene hunting with hidden Markov model knockoffs”. Biometrika 106(1): 23-26.
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2018
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Petersen and Witten (2018) Data-adaptive additive modeling. Statistics in Medicine 38(4): 583-600.
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Bis J et al. (2018) Whole exome sequencing study identifies novel rare and common Alzheimer’s-associated variants involved in ... Molecular Psychiatry.
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Witten, Fertig, Anandkumar, and Dean (2018) What’s in a name? The need to nip NIPS. NeurIPS Workshop on Critiquing and Correcting Trends in Machine Learning.
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2017
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Inoue et al. (2017) A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity. Genome Research 27(1): 38-52.
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Chen, Shojaie, and Witten (2017) Network reconstruction from high-dimensional ordinary ... Journal of the American Statistical Association 112(520): 1697-1707.
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Chen, Witten, and Shojaie (2017) Nearly assumptionless screening for the mutually-exciting multivariate Hawkes process. Electronic Journal of Statistics 11(1): 1207-1234.
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2016
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Tan, Ning, Witten, and Liu (2016) Replicates in high dimensions, with applications to latent variable graphical models. Biometrika 103(4): 761-777.
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Sheng, Witten, and Zhou (2016) Hypothesis testing for differentially-correlated features. Biostatistics 17(4): 677-691.
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Bien and Witten (2016) Penalized Estimation in Complex Models. Handbook of Big Data. CRC Press. Editors: Peter Buhlmann, Michael Kane, Petros Drineas, and Mark van der Laan.
2015
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Tan and Witten (2015) Statistical properties of convex clustering. Electronic Journal of Statistics 9: 2324-2327.
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Tan, Witten, and Shojaie (2015) The cluster graphical lasso for improved estimation of Gaussian graphical models. Computational Statistics and Data Analysis 85: 23-36.
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Chen, Witten, and Shojaie (2015) Selection and estimation in mixed graphical models. Biometrika 102(1): 47-64.
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2014
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Zare ... Witten, Blau, and Noble (2014) Inferring clonal composition from multiple sections of a breast cancer. PLOS Computational Biology 10(7): e1003073.oble
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Mohan, London, Fazel M, Witten D, and Lee (2014) Node-based learning of multiple Gaussian graphical models. Journal of Machine Learning Research 15: 445-488.
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Witten, Shojaie, and Zhang (2014) The cluster elastic net for high-dimensional regression with unknown variable grouping. Technometrics 56(1): 112-122.
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Tan, Petersen, and Witten (2014) Classification of RNA-Seq Data. Statistical Analysis of Next Generation Sequencing Data. Springer. Editors: Daniel Nettleton and Somnath Data.
Tay-Sontheimer et al. (2014) Detection of an endogenous urinary biomarker associated with CYP2D6 activity using global metabolomics. Pharmacogenomics 15(16): 1947-1962.
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Grechkin et al. (2014) Pathway Graphical Lasso. Twenty-Ninth AAAI Conference on Artificial Intelligence (AAAI-15).
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2013
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Witten (2013) Penalized unsupervised learning with outliers. Statistics and its Interface 6(2): 211-221.
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Zhao et al. (2013) Is GATA3 expression maintained in regional metastases? A study of paired primary and metastatic ... The American Journal of Surgical Pathology 37(12): 1876- 1881.
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Witten and Tibshirani (2013) Scientific research in the era of omics: the good, the bad, and the sloppy. Journal of the American Medical Informatics Association 20(1): 125-127.
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2012
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Witten and Noble (2012) On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements. Nucleic Acids Research 40(9): 3849-3855.
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Brunner et al. (2012) Transcriptional profiling of lncRNAs and novel transcribed region across a diverse panel of archived human cancers. Genome Biology 13(8):R75.
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Williams, Witten, Duester, and Chou (2012) The benefits of implant removal from the foot and ankle. Journal of Bone and Joint Surgery 94(14): 1316-1320.
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Patwardhan et al. (2012) Massively parallel functional dissection of mammalian enhancers in vivo. Nature Biotechnology 30(3): 265-270.
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Mohan et al. (2012) Structured sparse learning of Gaussian graphical models. Advances in Neural Information Processing Systems.
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Sung et al. (2012) Molecular signatures from omics data: from chaos to consensus. Biotechnology Journal 7(8): 946-957.
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Micheel et al; Institute of Medicine (2012) Evolution of Translational Omics: Lessons Learned and the Path Forward. National Academy of Sciences Press. 300 pages.
Maldonado et al. (2012) The Stanford Integrated Psychosocial Assessment for Transplantation (SIPAT): A New Tool for the ... Psychosomatics 53(2): 123-132.
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2011
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Li, Witten, Johnstone, and Tibshirani (2011) Normalization, testing, and false discovery rate estimation for RNA-sequencing data. Biostatistics 13(3): 523-538.
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Clemmensen, Hastie, Witten, and Ersboll (2011) Sparse discriminant analysis. Technometrics 53(4): 406-413.
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Witten and Tibshirani (2011) Supervised multidimensional scaling for visualization, classification, and bipartite ranking. Computational Statistics and Data Analysis 55(1): 789-801.
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Wu et al. (2011) Endogenous versus tumor-specific host response to breast carcinoma: a study of stromal response ... Clinical Cancer Research 17(3): 437-446.
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Ganjoo et al. (2011) The prognostic value of tumor associated macrophages in leiomyosarcoma: A single institution study. American Journal of Clinical Oncology 34(1): 82-86.
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2010
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Witten, Tibshirani, Gu, Fire, Lui (2010) Ultra-high throughput sequencing-based small RNA discovery ... BMC Biology 8(1): 58.
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Witten and Tibshirani (2010) Survival analysis with high-dimensional covariates. Statistical Methods in Medical Research 19(1): 29-51.
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Caramuta et al. (2010) MicroRNA expression profiles associated with mutational status and survival in malignant melanoma. Journal of Investigative Dermatology 130: 2062-2070.
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Jockers and Witten (2010) A comparative study of machine learning methods for authorship attribution. Literary and Linguistic Computing 25(2): 215-223.
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Beck et al. (2010) Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling. Oncogene 29: 845-854
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Beck et al. (2010) 3’-end sequencing for expression quantification (3SEQ) from archival tumor samples. PLoS ONE 5(1): e8768.
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2009
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Witten, Hastie, and Tibshirani (2009) Discussion of “On consistency and sparsity of principal components ...” Journal of the American Statistical Association 104(486): 698-699.
Somervaille et al. (2009) Hierarchical maintenance of MLL myeloid leukemia stem cells employs a transcriptional program shared ... Cell Stem Cell 4(2): 129-140.
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Jockers, Witten, and Criddle (2009) Reassessing the authorship of the Book of Mormon ... Literary and Linguistic Computing 23(4): 465-491.
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Brar et al. (2009) Breast angiosarcoma: case series and expression of vascular endothelial growth factor. Case Reports in Oncology 2: 242-250.
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2008
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Chou et al. (2008) Postoperative pain following foot and ankle surgery: a prospective study. Foot and Ankle International 29(11): 1064-1069
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Huang et al. (2008) A recoding method to improve the humoral immune response to an HIV DNA vaccine. PLoS ONE 3(9): e3214.
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Macpherson et al. (2008) Nonadaptive explanations for signatures of partial selective sweeps in Drosophila. Molecular Biology and Evolution 25(6): 1025-1042.
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