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Publications of the Center for Causal Discovery |
| 2020 |
| Xue Y, Ding MQ, Lu X. Learning to Encode Cellular Responses to Systematic Perturbations with Deep Generative Models. bioRxiv. Jan 1, 2020. |
| Liang L, Zhu K, Lu S. ORN: Extracting Latent Pathway Activities in Cancer with OR-gate Network. bioRxiv. Jan 1, 2020. |
| Verleden SE, Tanabe N, McDonough JE, Vasilescu DM, Xu F, Wuyts WA, Piloni D, De Sadeleer L, Willems S, Mai C, Hostens J, et al. Small airways pathology in idiopathic pulmonary fibrosis: a retrospective cohort study. The Lancet Respiratory Medicine. Feb 13, 2020. |
| Andrews B, Spirtes P, Cooper GF. On the Completeness of Causal Discovery in the Presence of Latent Confounding with Tiered Background Knowledge. In: Proceedings of the International Conference on Artificial Intelligence and Statistics. Jun 3, 2020. |
| Huang B, Zhang K, Gong M, Glymour C. Causal Discovery from Multiple Data Sets with Non-Identical Variable Sets. In: Proceedings of the Association for the Advancement of Artificial Intelligence. 2020. |
| Salehkaleybar S, Ghassami A, Kiyavash N, Zhang K. Learning Linear Non-Gaussian Causal Models in the Presence of Latent Variables. Journal of Machine Learning Research. Jan 1, 2020;21(39):1-24. |
| Adams TS, Schupp JC, Poli S, Ayaub EA, Neumark N, Ahangari F, Chu SG, Raby BA, DeIuliis G, Januszyk M, Duan Q, et al. Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis. Science Advances. Jul 1, 2020;6(28). |
| Ghassami A, Yang A, Kiyavash N, Zhang K. Characterizing Distribution Equivalence and Structure Learning for Cyclic and Acyclic Directed Graphs. In: Proceedings of the International Conference on Machine Learning. 2020. |
| Uttam S, Stern AM, Sevinsky CJ, Furman S, Pullara F, Spagnolo D, Nguyen L, Gough A, Ginty F, Taylor DL, Chennubhotla SC. Spatial domain analysis predicts risk of colorectal cancer recurrence and infers associated tumor microenvironment networks. Nature Communications. Jul 14, 2020;11(1):1-4. |
| Huang B, Zhang K, Zhang J, Ramsey J, Sanchez-Romero R, Glymour C, Schölkopf B. Causal discovery from heterogeneous/nonstationary data. Journal of Machine Learning Research. Jan 1, 2020;21(89):1-53. |
| 2019 |
| Huang B, Zhang K, Gong M, Glymour C. Causal Discovery and Forecasting in Nonstationary Environments with State-Space Models. In: Proceedings of the 36th International Conference on Machine Learning. PubMed PMID: 31497778: PubMed Central PMCID: PMC6730644. |
| Stojanov P, Gong M, Carbonell, JG, Zhang K. Low-Dimensional Density Ratio Estimation for Covariate Shift Correction. Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics (AISTATS) 2019. PubMed PMID: 31497776; PubMed Central PMCID: PMC6730633. |
| Stojanov P, Gong M, Carbonell, JG, Zhang K. Data-Driven Approach to Multiple-Source Domain Adaptation. Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics (AISTATS) 2019. Naha, Okinawa, Japan. PMLR: Volume 89. PubMed PMID: 31497777; PubMed Central PMCID: PMC6730632. |
| Malinsky D, Spirtes P. Learning the Structure of a Nonstationary Vector Autoregression. Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics (AISTATS) 2019. Naha, Okinawa, Japan. PMLR: Volume 89. NIHMSID: NIHMS1037086. |
| Ramsey JD, Zhang K, Glymour M, Sanchez Romero R, Huang B, Ebert-Uphoff I, Samarasinghe S, Barnes E, Glymour C. TETRAD – A Toolbox for Causal Discovery. 8th International Workshop on Climate Informatics. Long Beach CA. NIHMSID: NIHMS1017552. |
| Hu S, Zhang K, Chen Z, Chan L. Domain Generalization via Multidomain Discriminant Analysis. In: Proceedings of the Conference on Uncertainty in Artificial Intelligence, UAI 2019. Tel Aviv Israel , 26 July 2019. Available at: http://auai.org/uai2019/proceedings/papers/101.pdf. NIHMSID: NIHMS1048865. |
| Runge J, Bathiany S, Boolt E, Camps-Valls G, Coumou D, Deyle E, Glymour C, Kretschmer M, Mahecha MD, Munoz-Mari J, vanNes EH, Peters J, Quax R, Reichstein M, Scheffer M, Schölkopf B, Spirtes P, Sugihara G, Sun J, Zhang K, Zscheischler J. Inferring causation from time series in Earth system sciences. Nature Communications 10, Article 2553 , 2019 June 14;10(1):2553. doi: 10.1038/s41467-019-10105-3. Review. PubMed PMID: 31201306; PubMed Central PMCID: PMC6572812. |
| Schnetz MP, Hochheiser HS, Danks DJ, Landsittel DP, Vogt KM, Ibinson JW, Whitehurst SL, McDermott SP, Duque MG, Kaynar AM. The triple variable index combines information generated over time from common monitoring variables to identify patients expressing distinct patterns of intraoperative physiology. BMC Med Res Methodol. 2019 Jan 14;19(1):17. doi: 10.1186/s12874-019-0660-9. PubMed PMID: 30642260; PubMed Central PMCID: PMC6332613. |
| Liang L, Chen V, Zhu K, Fan X, Lu X, Lu S. Integrating data and knowledge to identify functional modules of genes: a multilayer approach. BMC Bioinformatics. 2019 May 2;20(1):225. doi: 10.1186/s12859-019-2800-y. PubMed PMID: 31046665; PubMed Central PMCID: PMC6498600. |
| Glymour C, Zhang K, Spirtes P. Review of Causal Discovery Methods Based on Graphical Models. Front Genet. 2019 Jun 4;10:524. doi: 10.3389/fgene.2019.00524. eCollection 2019. PubMed PMID: 31214249; PubMed Central PMCID: PMC6558187. |
| Andrews B, Ramsey J, Cooper GF. Learning High-dimensional Directed Acyclic Graphs with Mixed Data-types. Proc Mach Learn Res. 2019 Aug;104:4-21. PubMed PMID: 31453569; PubMed Central PMCID: PMC6709674. |
| Cai R, Li Z, Wei P, Qiao J, Zhang K, Hao Z. Learning Disentangled Semantic Representation for Domain Adaptation. In: Proceedings of the Twenty-Eighth International Joint Conference on Artificial Intelligence (IJCAI-19). 2019 Aug. Macao, China. NIHMSID: NIHMS1050423. |
| Xue Y, Cooper G, Cai C, Lu S, Hu B, Ma X, Lu X. Tumour-specific Causal Inference Discovers Distinct Disease Mechanisms Underlying Cancer Subtypes. Accepted to: Scientific Reports, September 2019. DOI : 10.1038/s41598-019-48318-7 |
| 2018 |
| Yang R, Spirtes P, Scheines R, Reise SP, Mansoff M. Finding Pure Sub-Models for Improved Differentiation of Bi-Factor and Second-Order Models. Structural equation modeling : a multidisciplinary journal. 2017;24(3):402-413. PubMed PMID: 29230085; PubMed Central PMCID: PMC5722276. |
| 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. PubMed PMID: 28328502; PubMed Central 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. PubMed PMID: 28334818; PubMed Central 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. PubMed PMID: 28231035 PubMed Central 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 Conference on Artificial Intelligence, Melbourne, Australia, August 19-25, 2017. PubMed PMID: 29203954; PubMed Central PMCID: PMC5617646. |
| 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. Available at: http://www.sciencedirect.com/science/article/pii/S0888613X17303882. PubMed PMID: 29203954; PubMed Central PMCID: PMC5711475. |
| Spagnolo DM, Al-Kofahi Y, Zhu P, Lezon TR, Gough A, Stern AM, Lee AV, Ginty F, Sarachan B, Taylor DL, Chennubhotla SC. Platform for Quantitative Evaluation of Spatial Intratumoral Heterogeneity in Multiplexed Fluorescence Images. Cancer research. 2017 November 1;77(21):e71-e74. PubMed PMID: 29092944; PubMed Central PMCID: PMC5683175. |
| Partha R, Chauhan BK, Ferreira Z, Robinson JD, Lathrop K, Nischal KK, Chikina M, Clark NL. Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling. Elife. 2017 Oct 16;6. pii: e25884. doi: 10.7554/eLife.25884. PubMed PMID: 29035697; PubMed Central PMCID: PMC5643096. |
| Chikina M, Robinson JD, Clark NL. Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals. Mol Biol Evol. 2016 Sep;33(9):2182-92. doi: 10.1093/molbev/msw112. Epub 2016 Jun 21. PubMed PMID: 27329977. PubMed Central PMCID: PMC5854031. |
| Andrews B, Ramsey J, Cooper G. Scoring Bayesian networks of mixed variables. International Journal of Data Science and Analytics. 2018 January 11; :1-16.PubMed PMID: 30140730; PubMed Central PMCID: PMC6101981. |
| Naeini MP, Cooper GF. Binary Classifier Calibration Using an Ensemble of Piecewise Linear Regression Models. Knowledge and information systems. 2017 November 17; :1-20. Pub Med PMID: 29606784; PubMed Central PMCID: PMC5875942 |
| Jabbari F, Ramsey J, Spirtes P, Cooper GF. Discovery of causal models that contain latent variables through Bayesian scoring of independence constraints. Proceeding of the European Conference on Machine Learning. 2017. PubMed PMID: 29520396; PubMed Central PMCID: PMC5836552. |
| Ding MQ, Chen L, Cooper GF, Young JD, Lu X. Precision Oncology beyond Targeted Therapy: Combining Omics Data with Machine Learning Matches the Majority of Cancer Cells to Effective Therapeutics. Mol Cancer Res. 2018 Feb;16(2):269-278. doi: 10.1158/1541-7786.MCR-17-0378. Epub 2017 Nov 13. PubMed PMID: 29133589; PubMed Central PMCID: PMC5821274. |
| Hyttinen A, Plis S, Järvisalo M, Eberhardt F, Danks D. A Constraint Optimization Approach to Causal Discovery from Subsampled Time Series Data. Int J Approx Reason. 2017 Nov;90:208-225. doi: 10.1016/j.ijar.2017.07.009. Epub 2017 Jul 29. PubMed PMID: 29755201; PubMed Central PMCID: PMC5944866. |
| Gong M, Zhang, K, SchÖlkopf B, Glymour 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. Available at: http://auai.org/uai2017/proceedings/papers/269.pdf PubMed PMID: 29899680; PubMed Central PMCID: PMC5995575. |
| Raghu VK, Ramsey JD, Morris A, Manatakis DV, Sprites P, Chryansthis 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. Available at: http://nugget.unisa.edu.au/CD2017/papersonly/comparisonStrategy-r1.pdf. PubMed PMID: 30148202; PubMed Central PMCID: PMC6096780. |
| Wenzel SE, Tyurina YY, Zhao J, St Croix CM, Dar HH, Mao G, Tyurin VA, Anthonymuthu TS, Kapralov AA, Amoscato AA, Mikulska-Ruminska K, Shrivastava IH, Kenny EM, Yang Q, Rosenbaum JC, Sparvero LJ, Emlet DR, Wen X, Minami Y, Qu F, Watkins SC, Holman TR, VanDemark AP, Kellum JA, Bahar I, Bayır H, Kagan VE. PEBP1 Wardens Ferroptosis by Enabling Lipoxygenase Generation of Lipid Death Signals.Cell. 2017 Oct 19;171(3):628-641.e26. doi: 10.1016/j.cell.2017.09.044. PubMed PMID: 29053969; PubMed Central PMCID: PMC5683852. |
| Chennubhotla C, Clarke LP, Fedorov A, Foran D, Harris G, Helton E, Nordstrom R, Prior F, Rubin D, Saltz JH, Shalley E, Sharma A. An Assessment of Imaging Informatics for Precision Medicine in Cancer. Yearb Med Inform. 2017 Aug;26(1):110-119. doi: 10.15265/IY-2017-041. Epub 2017 Sep 11. PubMed PMID: 29063549; PubMed Central PMCID: 6250996. |
| Young JD, Cai C, Lu X. Unsupervised deep learning reveals prognostically relevant subtypes of glioblastoma. BMC Bioinformatics. 2017 Oct 3;18(Suppl 11):381. doi: 10.1186/s12859-017-1798-2. PubMed PMID: 28984190; PubMed Central PMCID: PMC5629551. |
| Yang R, Spirtes P, Scheines R, Reise SP, Mansoff M. Finding Pure Sub-Models for Improved Differentiation of Bi-Factor and Second-Order Models. Structural equation modeling : a multidisciplinary journal. 2017;24(3):402-413. PubMed PMID: 29230085; PubMed Central PMCID: PMC5722276. |
| Danks D, Plis S. Amalgamating evidence of dynamics. Synthese (2017).First Online: 18 September 2017. https://doi.org/10.1007/s11229-017-1568-8 NIHMSID: NIHMS932970 |
| Biwei Huang, Kun Zhang, Jiji Zhang, Ruben Sanchez-Romero, Clark Glymour, Bernhard Scholkopf, Behind Distribution Shift: Mining Driving Forces of Changes and Causal Arrows, 2017 IEEE International Conference on Data Mining (ICDM), 913-918, 2017, doi:10.1109/ICDM.2017.114. PubMed PMID: 31068766; PubMed Central PMCID: PMC6502242. |
| Naeini MP, Jabbari F, Cooper GF. An Assessment of the Calibration of Causal Relationships Learned Using RFCI and Bootstrapping. 4th Workshop on Data Mining for Medical Informatics: Casual Inference for Health Data Analytics. 2017 November 04. PMC not applicable. |
| Wang Q, MIskov-Zivanov N, Liu B, Faeder JR, Lotze M, Clarke EM. In: Computational Methods in Systems Biology. Bartocci E, Lio P, Paoletti N, editors. Cambridge UK. Springer International Publishing; 2016. Formal Modeling and Analysis of Pancreatic Cancer Microenvironment; 289-305p. 356p. PMC not applicable |
| Wang M, Zheng X, Yang Y, Khang K. Collaborative Filtering with Social Exposure: A Modular Approach to Social Recommendation. [Internet]. arXiv.org2017 November. Available from: https://arxiv.org/abs/1711.11458. |
| 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. Available at: https://arxiv.org/pdf/1705.09031.pdf |
| Huang B, Zhang K, Lin Y, Schölkopf B, Glymour C. Generalized Score Functions for Causal Discovery. KDD. 2018 Aug;2018:1551-1560. doi: 10.1145/3219819.3220104. PubMed PMID: 30191079; PubMed Central PMCID: PMC6123020. |
| Lu S, Fan X, Chen L, Lu X. A novel method of using Deep Belief Networks and genetic perturbation data to search for yeast signaling pathways. PLoS One. 2018 Sep 12;13(9):e0203871. doi: 10.1371/journal.pone.0203871. eCollection 2018. PubMed PMID: 30208101; PubMed Central PMCID: PMC6135403. |
| Ponzoni L, Bahar I. Structural dynamics is a determinant of the functional significance of missense variants. Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):4164-4169. doi: 10.1073/pnas.1715896115. Epub 2018 Apr 2. PubMed PMID: 29610305, PubMed Central PMCID: PMC5910821. |
| Meyer WK, Jamison J, Richter R, Woods SE, Partha R, Kowalczyk A, Kronk C, Chikina M, Bonde RK, Crocker DE, Gaspard J, Lanyon JM, Marsillach J, Furlong CE, Clark NL. Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals. Science. 2018 Aug 10;361(6402):591-594. doi: 10.1126/science.aap7714. PubMed PMID: 30093596. PubMed Central PMCID: PMC6317340. |
| Sedgewick AJ, Buschur K, Shi I, Ramsey JD, Raghu VK, Manatakis DV, Zhang Y, Bon J, Chandra D, Karoleski C, Sciurba FC, Spirtes P, Glymour C, Benos PV. Mixed Graphical Models for Integrative Causal Analysis with Application to Chronic Lung Disease Diagnosis and Prognosis. Bioinformatics. 2018 Sep 5. doi: 10.1093/bioinformatics/bty769. [Epub ahead of print] PubMed PMID: 30192904. PubMed Central PMCID: PMC6449754 [Available on 2020-04-01] |
| Ponzoni L, Bahar I. Structural dynamics is a determinant of the functional significance of missense variants. Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):4164-4169. doi: 10.1073/pnas.1715896115. Epub 2018 Apr 2. PubMed PMID: 29610305; PubMed Central PMCID: PMC5910821. |
| Strobl EV, Visweswaran S, Spirtes PL. Fast Causal Inference with Non-Random Missingness by Test-Wise Deletion. Int J Data Sci Anal. 2018 Aug;6(1):47-62. doi: 10.1007/s41060-017-0094-6. Epub 2018 Jan 19. PubMed PMID: 31321289; PubMed Central PMCID: PMC6638553. |
| Sanchez-Romero R, Ramsey JD, Zhang K, Glymour MR. Estimating Feedforward and Feedback Effective Connections from 2 FMRI Time Series: Assessments of Statistical Methods. Network neuroscience (Cambridge, Mass.). 2018 June 04; :1-33. 1 PubMed PMID: 30793083; PubMed Central PMCID: PMC6370458. |
| Ponzoni L, Zhang S, Cheng MH, Bahar I. Shared dynamics of LeuT superfamily members and allosteric differentiation by structural irregularities and multimerization. Philos Trans R Soc Lond B Biol Sci. 2018 Jun 19;373(1749). pii: 20170177. doi: 10.1098/rstb.2017.0177. PubMed PMID: 29735731; PubMed Central PMCID: PMC5941172. |
| Jabbari F, Visweswaran S, Cooper GF. Instance-Specific Bayesian Network Structure Learning. Proc Mach Learn Res. 2018 Sep;72:169-180. PubMed PMID: 30775723; PubMed Central PMCID: PMC6376975. |
| Schnetz MP, Hochheiser HS, Danks DJ, Landsittel DP, Vogt KM, Ibinson JW, Whitehurst SL, McDermott SP, Duque MG, Kaynar AM. The triple variable index combines information generated over time from common monitoring variables to identify patients expressing distinct patterns of intraoperative physiology. BMC Med Res Methodol. 2019 Jan 14;19(1):17. doi: 10.1186/s12874-019-0660-9. PubMed PMID: 30642260; PubMed Central PMCID: PMC6332613. |
| Chen, L. and Lu, X. Discovering functional impact of microRNAs in cancer using a causal deep learning model. (doi: 10.1186/s12920-018-0432-0). Proceedings of the 29th International Conference on Genome Informatics (GIW 2018): Medical Genomics. BMC Medical Genomics 2018 Dec 31;11(Suppl 6):116. doi: 10.1186/s12920-018-0432-0. PubMed PMID: 30598118; PubMed Central PMCID: PMC6311958. |
| Wang M, Gong M, Zhang K, Zheng X. Modeling Dynamic Missingness of Implicit Feedback for Recommendation. Proceedings of the 32nd Conference on Neural Information Processing Systems (NIPS 2018), Montréal, Canada.. 2018 December. PubMed PMID: 30971864; PubMed Central PMCID: PMC6453574. |
| Cai R, Qiao J, Zhang K, Zhang Z, Ha Z. Causal Discovery from Discrete Data using Hidden Compact Representation. 2018. In Proceedings of 2nd Conference on Neural Information Processing Systems (NIPS 2018), Montréal, Canada. Adv Neural Inf Process Syst. 2018 Dec; 2666-2674. PubMed PMID: 30956519; PubMed Central PMCID: PMC6448794. |
| Ghassami A, Kiyavash N, Huang B, Zhang K. Multi-domain Causal Structure Learning in Linear Systems. Adv Neural Inf Process Syst. 2018 Dec;31:6266-6276. PubMed PMID: 30971863; PubMed Central PMCID: PMC6453575. |
| Huang B, Zhang K, Zhang J, Sanchez-Romero R, Glymour C, Scholkopf B. Behind Distribution Shift: Mining Driving Forces of Changes and Causal Arrows. In Proceedings of the 2017 IEEE International Conference on Data Mining. PubMed PMID: 31068766; PubMed Central PMCID: PMC6502242. |
| Zhang K, Schölkopf B, Spirtes P, Glymour C. Learning causality and causality-related learning: some recent progress. Natl Sci Rev. 2018 Jan;5(1):26-29. doi: 10.1093/nsr/nwx137. Epub 2017 Nov 17. PubMed PMID: 30034911; PubMed Central PMCID: PMC6051411. |
| Ramsey JD, Zhang K, Glymour M, Sanchez Romero R, Huang B, Ebert-Uphoff I, Samarasinghe S, Barnes EA, Glymour C. Tetrad – A Toolbox for Causal Discovery. 8th International Workshop on Climate Informatics, September 19-21, 2018, Boulder CO. NIHMSID: NIHMS1017552. |
| 2017 |
| Haliloglu T, Bahar I. Adaptability of protein structures to enable functional interactions and evolutionary implications. Current opinion in structural biology. 2015 December; 35:17-23. PubMed PMID: 26254902; PubMed Central PMCID: PMC4688206. |
| Kummerfeld E, Ramsey J. Causal Clustering for 1-Factor Measurement Models. KDD : proceedings. International Conference on Knowledge Discovery & Data Mining. 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 PMID: 28217244; 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 Conf Proc. 2016 Aug;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. PubMed PMID: 28239433; PubMed Central PMCID: PMC5321138. |
| 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; PubMed Central PMCID: PMC5854031. |
| 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. PubMed PMID: 28393106; PubMed Central PMCID: PMC5380925. |
| Naeini MP, Cooper GF. Binary Classifier Calibration using an Ensemble of Near Isotonic Regression Models. Proceedings of ICDM 2016, IEEE International Conference on Data Mining. 2016. PubMed PMID: 28316511; PubMed Central PMCID: PMC5351887. |
| 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. PubMed PMID: 28239434; PubMed Central 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. PubMed PMID: 28363452; PubMed Central PMCID: PMC5415921. |
| Nguyen L, Tosun AB, Fine JL, Taylor DL, 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. http://ieeexplore.ieee.org/document/7950490/. PubMed PMID: 28890755; PubMed Central PMCID: PMC5589141. |
| 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. PubMed PMID: 28280453; PubMed Central PMCID: PMC5340263. |
| Young JD, Cai C, Lu X. Unsupervised Deep Learning Reveals Prognostically Relevant Subtypes of Glioblastoma. BMC Bioinformatics. 2017 Oct 3;18(Suppl 11):381. doi: 10.1186/s12859-017-1798-2. PubMed PMID: 28984190; PubMed Central PMCID: PMC5629551. |
| 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. bioRxiv 068841; doi: https://doi.org/10.1101/068841. |
| Sanchez-Romero R, Ramsey J, Liang JC, Glymour C. Identification of Mechanisms of Functional Signaling Between Human Hippocampus Regions. 2016 December. bioRxiv 099820; doi: ttps://doi.org/10.1101/099820. |
| Wang Q., Miskov-Zivanov N., Liu B., Faeder J.R., Lotze M., Clarke E.M. (2016) Formal Modeling and Analysis of Pancreatic Cancer Microenvironment. In: Bartocci E., Lio P., Paoletti N. (eds) Computational Methods in Systems Biology. CMSB 2016. Lecture Notes in Computer Science, vol 9859. Springer, Cham. doi: 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 EricV, 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. |
| 2016 |
| Chen L, Cai C, Chen V, Lu X. Trans-species learning of cellular signaling systems with bimodal deep belief networks. Bioinformatics. 2015 Sep 15;31(18):3008-15. PubMed PMID: 25995230; PubMed Central PMCID: PMC4668779. |
| Chikina M, Zaslavsky E, Sealfon SC. CellCODE: a robust latent variable approach to differential expression analysis for heterogeneous cell populations. Bioinformatics. 2015 May 15;31(10):1584-91. PubMed PMID: 25583121; PubMed Central PMCID: PMC4426841. |
| 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. |
| Pils S, Danks D, Yang J. Mesochronal structure learning. In: Proceedings of Uncertainty in Artificial Intelligence 2015 UAI Press, 702-11. PubMed PMID: 27076793; PubMed Central PMCID: PMC4827356. |
| Plis S, Danks D, Freeman C, Calhoun V. Rate-Agnostic (Causal) Structure Learning. In: Advances in Neural Information Processing Systems 2015 (pp. 3285-3293). PubMed PMID: 27182188; PubMed Central PMCID: PMC4863709. |
| Visweswaran S, Ferreira A, Ribeiro GA, Oliveira AC, Cooper GF. Personalized Modeling for Prediction with Decision-Path Models. PLoS One. 2015;10(6):e0131022. PubMed PMID: 26098570; PubMed Central PMCID: PMC4476684. |
| 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. |
| Spirtes P, Zhang K. Causal Discovery and Inference: Concepts and Recent Methodological Advances. Applied Informatics. PubMed PMID: 27195202; PubMed Central PMCID: PMC4841209. |
| Murray-Watters A, Glymour C. What’s Going on Inside the Arrows? Discovering the Hidden Springs in Causal Models. Philosophy of Science. PubMed PMID: 27313331; PubMed Central PMCID: PMC4905594. |
| Strobl EV, Visweswaran S. Markov boundary discovery with ridge regularized linear models. Journal of Causal Inference. PubMed PMID: 27170915; PubMed Central PMCID: PMC4861166. |
| 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. |
| 2015 |
| 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. Pac Symp Biocomput. 2015; PubMed PMID: 25592602; PubMed Central PMCID: PMC4299881. |
| 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. |
| Lu S, Lu KN, Cheng SY, Hu B, Ma X, Nystrom N, Lu X. Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets. PLoS Comput Biol. 2015 Aug;11(8):e1004257. PubMed PMID: 26317392; PubMed Central PMCID: PMC4552843. |