CCD Members

2017

Raghu VK, Ramsey JD, Morris A, Manatakis DV, Sprites P, Chrysanthis PK, Glymour C,  Panayiotis BV.  Comparison of Strategies for Scalable Causal Discovery of Latent Variable Models from Mixed Data. Proceedings: 2017 ACM SIGKDD Workshop on Causal Discovery, Halifax, Nova Scotia, Canada, August 14, 2017.

Malinsky D. Spirtes P. Estimating bounds on causal effects in high-dimensional and possibly confounded systems. International Journal of Approximate Reasoning, vol 88 September 2017, 371-84.

Strobl EV, Visweswaran S. Spirtes PL. Fast Causal Inference with Non-Random Missingness by Test-Wise Deletion. arXiv:1705.09031v1  [stat.ME]  25 May 2017.

Nguyen L, Tosun AB, Fine JL, Lee AV, Taylor DL, Chennubhotla SC. Spatial Statistics for Segmenting Histological Structures in H&E Stained Tissue Images. IEEE Trans Med Imaging. 2017 Jul;36(7):1522-1532. doi: 10.1109/TMI.2017.2681519. Epub 2017 Mar 16. PMID: 28328502 PMCID: PMC5498226

Sauerwald N, Zhang S, Kingsford C, Bahar I. Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings. Nucleic Acids Res. 2017 Apr 20;45(7):3663-3673. doi: 10.1093/nar/gkx172. PMCID: PMC5397156

Gough A, Stern AM, Maier J, Lezon T, Shun TY, Chennubhotla C, Schurdak ME, Haney SA, Taylor DL. Biologically Relevant Heterogeneity: Metrics and Practical Insights. SLAS Discov. 2017 Mar;22(3):213-237. doi: 10.1177/2472555216682725. Epub 2017 Jan 6.  DOI: 10.1177/2472555216682725 PMID: 28231035 PMCID: PMC5464733 

Zhang K, Huang B, Zhang J, Glymour C, SchÖlkopf B. Causal Discovery from Nonstationary/Heterogeneous Data: Skeleton Estimation and Orientation Determination.  Proceedings: International Joint Converence on Aritifical Intelligence, Melbourne, Australia, August 19-25, 2017.

Gong M, Zhang, K, SchÖlkopf B, Glyour C, Tao D. Causal Discovery from Temporally Aggregated Time Series. Proceedings: Conference on Uncertainty in Artificial Intelligence (UAI’17). Sydney, Australia, August 11-15, 2017.


2016

Kummerfeld E, Ramsey J. Causal Clustering for 1-Factor Measurement Models. KDD : proceedings. International Conference on Knowledge Discovery & Data Mining. 2016;2016:1655-1664. PubMed PMID: 27766182; PubMed Central PMCID: PMC5066593.

Malinsky D, Sprites P. Estimating Causal Effects with Ancestral Graph Markov Models. JMLR: Workshop and Conference Proceedings; PGM 2016. 2016;52:299-309. PubMed Central PMCID: PMC5313053.

Sedgewick AJ, Shi I, Donovan RM, Benos PV. Learning mixed graphical models with separate sparsity parameters and stability-based model selection. BMC bioinformatics. 2016 June 6;17 Suppl 5:175. PubMed PMID: 27294886; PubMed Central PMCID: PMC4905606.

Hyttinen A, Plis S, Järvisalo M, Eberhardt F, Danks D. Causal Discovery from Subsampled Time Series Data by Constraint Optimization. JMLR workshop and conference proceedings. 2016 August;52:216-227. PubMed PMID: 28203316; PubMed Central PMCID: PMC5305170.

Huang T, Alvarez AA, Pangeni RP, M Horbinski C, Lu S, Kim SH, James CD, J Raizer J, A Kessler J, Brenann CW, Sulman EP, Finocchiaro G, Tan M, Nishikawa R, Lu X, Nakano I, Hu B, Cheng SY. A regulatory circuit of miR-125b/miR-20b and Wnt signalling controls glioblastoma phenotypes through FZD6-modulated pathways. Nature communications. 2016 October 4;7:12885. PubMed PMID: 27698350; PubMed Central PMCID: PMC5059456.

Spagnolo DM, Gyanchandani R, Al-Kofahi Y, Stern AM, Lezon TR, Gough A, Meyer DE, Ginty F, Sarachan B, Fine J, Lee AV, Taylor DL, Chennubhotla SC. Pointwise mutual information quantifies intratumor heterogeneity in tissue sections labeled with multiple fluorescent biomarkers. Journal of pathology informatics. 2016 November 29;7:47. PubMed PMID: 27994939; PubMed Central PMCID: PMC5139455.

Lu S, Cai C, Yan G, Zhou Z, Wan Y, Chen V, Chen L, Cooper GF, Obeid LM, Hannun YA, Lee AV, Lu X. Signal-Oriented Pathway Analyses Reveal a Signaling Complex as a Synthetic Lethal Target for p53 Mutations. Cancer research. 2016 December 1;76(23):6785-6794. PubMed PMID: 27758891; PubMed Central PMCID: PMC5165695.

Zhou Z, Luo A, Shrivastava I, He M, Huang Y, Bahar I, Liu Z, Wan Y. Regulation of XIAP Turnover Reveals a Role for USP11 in Promotion of Tumorigenesis. EBioMedicine. 2017 February;15:48-61. PubMed PMID: 28040451; PubMed Central PMCID: PMC5233825.

Gong M, Zhang Kun, Liu T, Tao D, Glymour C, Scholkopf B. Domain Adaptation with Conditional Transferable Components. Proceedings of The 33rd International Conference on Machine Learning, JMLR: W&CP. 2016;48. PMCID: 5321138

Chikina M, Robinson JD, Clark NL. Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals. Molecular biology and evolution. 2016 September;33(9):2182-92. PubMed PMID: 27329977.

Ramsey J, Glymour M, Sanchez-Romero R, et. al. A million variables and more: the Fast Greedy Equivalence Search algorithm for learning high-dimensional graphical causal models, with an application to functional magnetic resonance images. International Journal of Data Science and Analytics. 2016 December 01. PMID: 28393106

Chen V, Paisley J, Lu X. Revealing common disease mechanisms shared by tumors of different tissues of origin through semantic representation of genomic alterations and topic modeling. BMC Genomics.BMC Genomics. 2017 Mar 14;18(Suppl 2):105. doi: 10.1186/s12864-017-3494-z. PMCID: PMC5374647. PMID: 28361690

Naeini MP, Cooper GF. Binary Classifer Calibration Using an Ensemble of Linear Trend Estimation. Proc SIAM Int Conf Data Min. 2016. PMCID: PMC5367639

Naeini MP, Cooper GF. Binary Classifier Calibration using an Ensemble of Near Isotonic Regression Models. Proceedings of ICDM 2016, IEEE International Confrence on Data Mining. 2016.

Ogarrio J, Spirtes P, Ramsey J. A Hybrid Causal Search Algorithm for Latent Variable Models. IN: JMLR Workshop and Conference Proceedings; From: International Conference on Probabilistic Graphical Models (PGM). 2016;52:368-79. PMCID: PMC5325717

Rathnam C, Lee S, Jiang Xia. An algorithm for direct causal learning of influences on patient outcomes. Artificial intelligence in medicine. 2016 November 05;75:1-15. PMCID: PMC5415921

Nguyen L, Tosun AB, Fine JL, Taylor L, Chennubhotla SC. Architectural patterns for differential diagnosis of proliferative breast lesions from histopathological images. 2017 IEEE 14th International Symposium on Biomedical Imaging, (ISBI 2017), Melbourne, VIC, 2017, pp.152-.155. doi:10.1109/ISBI.2017.7950490. NIHMSID 852397.

Scheines R, Ramsey J. Measurement Error and Causal Discovery. Proceedings of the UAI 2016 Workshop on Causation: Foundation to Application co-located with the 32nd Conference on Uncertainty in Artificial Intelligence (UAI 2016) Jersey City, USA. 2017 February 08;CEUR-WS.org Vol 1792. PMCID: PMC5340263

Hanson SJ, Mastrovito D, Hanson C, Ramsey J, Glymour C. Scale-Free Exponents of Resting State are Biomarkers of Neuro-Typical and Atypical Brain Activity. bioRxiv preprint. 2016 August 10.

Sanchez-Romero R, Ramsey J, Liang JC, Glymour C. Identification of Mechanisms of Functional Signaling Between Human Hippocampus Regions. bioRxiv preprint online. 2016 December.

Wang Q, Miskov-Zivanov N, Liu Bing, Faeder JR., Lotze M, Clarke EM. Formal Modeling and Analysis of Pancreatic Cancer Microenvironment. [Internet]. 16 pages. Available from: https://arxiv.org/abs/1606.03138.

Malinsky D, Spirtes P. Estimating Causal Effects with Ancestral Graph Markov Models. [Internet]. Pittsburgh PA: Technical Report No. CMU-PHIL-194; 2016 July 13. Available from: https://www.cmu.edu/dietrich/philosophy/docs/tech-reports/194_-malinsky.pdf.

Ramsey JD, Malinsky D. Comparing the Performance of Graphical Structure Learning Algorithms with TETRAD. [Internet]. Technical report: 22 pages. Available from: https://arxiv.org/pdf/1607.08110.pdf.

Strobl Eric, Visweswaran S, Zhang Kun. Approximate Kernel-based Conditional Independence Tests for Fast Non-Parametric Causal Discovery. [Internet]. 25 pages. Available from: https://arxiv.org/pdf/1702.03877.pdf.

Maathuis MH, Nandy P (2016) A review of some recent advances in causal inference. In P. Bühlmann, P. Drineas, M. Kane and M.J. van der Laan (Eds.), Handbook of Big Data, pp 387-407. Chapman and Hall/CRC, Boca Raton, FL. (arXiv:1506.07669)


2015

Bonifay W E, Reise SP, Scheines R, Meijer RR. When are multidimensional data unidimensional enough for structural equation modeling? An evaluation of the DETECT multidimensionality index. Structural Equation Modeling: A Multidisciplinary Journal 2015;22(4):504-516.

Chen L, Cai C, Chen V, Lu, X. Trans-species learning of cellular signaling systems with bimodal deep belief networks.  Bioinformatics 2015;31:3008-15. doi: 10.1093/bioinformatics/btv315. Epub 2015 May 20. PMID: 25995230

Chikina M, Zaslavsky E, Sealfon SC. CellCODE: a robust latent variable approach to differential expression analysis for heterogeneous cell populations. Bioinformatics 2015;31:1584-91; doi: 10.1093/bioinformatics/btv015. Epub 2015 Jan 11. PMCID: PMC4426841 [Available on 2016-05-15]

Cooper GF, Bahar I, Becich MJ, Benos PV, Berg J, Espino JU, Glymour C, Jacobson RC, Kienholz ML, Lee AV, Lu X, Scheines R. The Center for Causal Discovery of Biomedical Knowledge from Big Data. J Am Med Informatics Assoc 2015;1-6. doi: 10.1093/jamia/ocv059. PMID: 26138794

Glymour C, Hanson C. Reverse Inference in Neuropsychology. British Journal for the Philosophy of Science 2015;0:1-15. doi: 10.1093/bjps/axv019

Huang GT, Tsamardinos I, Raghu V, Kaminski N, Benos PV. T-ReCS: stable selection of dynamically formed groups of features with application to prediction of clinical outcomes. Pacific Symposium on Biocomputing 2015; 431-42. PMCID: PMC4299881 [Available on 2016-01-01]

Lu S, Lu KN Cheng S, Ma X, Nystrom NLu X. Identifying driver genomic alterations in cancers by searching minimum-weight, mutually exclusive sets.  PLoS Computational Biology 2015;11(8):e1004257. doi: 10.1371/journal.pcbi.1004257. eCollection 2015. PMCID: PMC4552843

Murray-Watters A, Glymour C. What’s going on inside the arrows? Discovering the hidden springs in causal models. Philosophy of Science 2014; doi 10.1086/682962.

Plis S, Danks D, Yang J. Mesochronal structure learning. In: Meila M, Heskes T (Eds.). Uncertainty in Artificial Intelligence 31 (UAI-2015) Corvallis, OR: AUAI Press, 2015;702-711. [first two authors contributed equally]

Ramsey J. Scaling Up Greedy Equivalent Search for Continuous Variables. Technical Report. arXiv:1507.07749 [cs.AI], 2015.

Strobl EV, Visweswaran S. Dependence versus conditional dependence in local causal discovery from gene expression data. arXiv:1407.7566, 2014

Strobl EV, Visweswaran S. Markov blanket ranking using kernel-based conditional dependence measures. arXiv:1402.0108, 2014

Strobl EV, Visweswaran S. Markov boundary discovery with ridge regularized linear models. Journal of Causal Inference 2015; doi 10.1515/jci-2015-0011.

Visweswaran S, Ferreira A, Cooper GF. Personalized modeling for prediction with decision-path models. PLoS One 2015 Jun 22;10(6):e0131022. PMID: 26098570 PMCID: PMC4476684

Lu S, Mandava G, Yan G, Lu X. An exact algorithm for finding cancer driver somatic genome alterations: the weighted mutually exclusive maximum set cover problem. Algorithms Mol Biol. 2016 May 4;11:11. doi: 10.1186/s13015-016-0073-9. eCollection 2016. PubMed PMID: 27148394; PubMed Central PMCID: PMC4855522.

Haliloglu T, Bahar I. Adaptability of protein structures to enable functional interactions and evolutionary implications. Curr Opin Struct Biol. 2015 Dec;35:17-23. PubMed PMID: 26254902; PubMed Central PMCID: PMC4688206.

Hu D, Gur M, Zhou Z, Gamper A, Hung MC, Fujita N, Lan L, Bahar I, Wan Y. Interplay between arginine methylation and ubiquitylation regulates KLF4-mediated genome stability and carcinogenesis. Nat Commun. 2015 Sep 30;6:8419. PubMed PMID: 26420673; PubMed Central PMCID: PMC4598737.

Priedigkeit N, Wolfe N, Clark NL. Evolutionary signatures amongst disease genes permit novel methods for gene prioritization and construction of informative gene-based networks. PLoS Genet. 2015 Feb;11(2):e1004967. PubMed PMID: 25679399; PubMed Central PMCID: PMC4334549.

Wolfe NW, Clark NL. ERC analysis: web-based inference of gene function via evolutionary rate covariation. Bioinformatics. 2015 Dec 1;31(23):3835-7. PubMed PMID: 26243019; PubMed Central PMCID: PMC4751245.

Naeini MP, Cooper GF, Hauskrecht M. Binary Classifier Calibration Using a Bayesian Non-Parametric Approach. Proc SIAM Int Conf Data Min. 2015;2015:208-216. PubMed PMID: 26613068; PubMed Central PMCID: PMC4657569.

Plis S, Danks D, Freeman C, Calhoun V. Rate-Agnostic (Causal) Structure Learning. In: Advances in Neural Information Processing Systems 2015 (pp. 3285-3293). PMCID: PMC4863709

Spirtes P, Zhang K. Causal Discovery and Inference: Concepts and Recent Methodological Advances. Applied Informatics.PMCID: PMC4841209