Cross-corpora unsupervised learning of trajectories in autism spectrum disorders

Journal of Machine Learning Research

Volumn 17, Issue , 2016, Pages 1-38

  Elibol, Huseyin Melih ^a   Nguyen, Vincent ^a   Linderman, Scott ^a   Johnson, Matthew ^a   Hashmi, Amna ^a   Doshi Velez, Finale ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

Disease progression model; Dynamic topic model

Indexed keywords

DISEASES; RECORDS MANAGEMENT; SOCIAL NETWORKING (ONLINE); TRAJECTORIES; UNSUPERVISED LEARNING;

AUTISM SPECTRUM DISORDERS; DEVELOPMENTAL DISORDERS; DISEASE PROGRESSION; DYNAMIC TOPIC MODELS; ELECTRONIC HEALTH RECORD; LANGUAGE IMPAIRMENTS; MULTIPLE DATA SOURCES; UNSUPERVISED APPROACHES;

DIAGNOSIS;

EID: 84989168006     PISSN: 15324435     EISSN: 15337928     Source Type: Journal    
DOI: None     Document Type: Article

References (101)

1. Ida Anjomshoaa, Margaret E Cooper, and Alexandre R Vieira. Caries is associated with asthma and epilepsy. European journal of dentistry, 3(4):297, 2009.
2. Jon Baio. Prevalence of autism spectrum disorders among children aged 8 years - autism and developmental disabilities monitoring network, 11 sites, united states, 2010. CDC Morbidity and Mortality Weekly Report, 63:1-21, March 2014.
3. M. L. Bauman. Medical comorbidities in autism: challenges to diagnosis and treatment. Neurotherapeutics, 7:320327., 2010.
4. Kevin G Becker. Autism, asthma, inflammation, and the hygiene hypothesis. Medical hypotheses, 69(4):731-740, 2007.
5. David Belanger and Sham Kakade. A linear dynamical system model for text. In Proceedings of the International Conference on Machine Learning, 2015.
6. A. Ben-Sasson, S. A. Cermak, G. I. Orsmond, H. Tager-Flusberg, M. B. Kadlec, and A. S. Carter. Sensory clusters of toddlers with autism spectrum disorders: differences in affective symptoms. J Child Psychol Psychiatry., 49(8):817-25, Aug 2008.
7. David A Beuther, Scott T Weiss, and E Rand Sutherland. Obesity and asthma. American Journal of Respiratory and Critical Care Medicine, 174(2):112-119, 2006.
8. V. Bitsika, C. F. Sharpley, and S. Orapeleng. An exploratory analysis of the use of cognitive, adaptive and behavioural indices for cluster analysis of asd subgroups. J Intellect Disabil Res., 52(11):973-85, Nov 2008.
9. David Blei and John Lafferty. Correlated topic models. Advances in neural information processing systems, 18:147, 2006a.
10. David M Blei and John D Lafferty. Dynamic topic models. In Proceedings of the International Conference on Machine Learning, pages 113-120. ACM, 2006b.
11. David M Blei, Andrew Y Ng, and Michael I Jordan. Latent dirichlet allocation. the Journal of machine Learning research, 3:993-1022, 2003.
12. O. Bodenreider. The unified medical language system (UMLS): integrating biomedical terminology. Nucleic acids research, 32:D267-D270, 2004.
13. Coleen A Boyle, Sheree Boulet, Laura A Schieve, Robin A Cohen, Stephen J Blumberg, Marshalyn Yeargin-Allsopp, Susanna Visser, and Michael D Kogan. Trends in the prevalence of developmental disabilities in us children, 1997-2008. Pediatrics, pages peds-2010, 2011.
14. Z. Che, D. Kale, W. Li, M. T. Bahadori, and Y. Liu. Deep computational phenotyping. In ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2015.
15. Brant W Chee, Richard Berlin, and Bruce Schatz. Predicting adverse drug events from personal health messages. In AMIA Annual Symposium Proceedings, volume 2011, page 217. American Medical Informatics Association, 2011.
16. Jianfei Chen, Jun Zhu, Zi Wang, Xun Zheng, and Bo Zhang. Scalable inference for logistic-normal topic models. In Advances in Neural Information Processing Systems (NIPS), pages 2445-2453, 2013.
17. Freddy Chong Tat Chua, Richard J Oentaryo, and Ee-Peng Lim. Using linear dynamical topic model for inferring temporal social correlation in latent space. arXiv preprint arXiv:1501.01270, 2015.
18. Glen Coppersmith, Mark Dredze, Craig Harman, Kristy Hollingshead, and Margaret Mitchell. Clpsych 2015 shared task: Depression and ptsd on twitter. In NAACL Workshop on Computational Linguistics and Clinical Psychology, 2015.
19. D. Coury. Medical treatment of autism spectrum disorders. Curr Opin Neurol, 23:131136, 2010.
20. Willem De Winter, Joost DeJongh, Teun Post, Bart Ploeger, Richard Urquhart, Ian Moules, David Eckland, and Meindert Danhof. A mechanism-based disease progression model for comparison of long-term effects of pioglitazone, metformin and gliclazide on disease processes underlying type 2 diabetes mellitus. Journal of pharmacokinetics and pharmacodynamics, 33(3):313-343, 2006.
21. G. Robert DeLong and Judith T. Dwyer. Correlation of family history with specific autistic subgroups: Asperger's syndrome and bipolar affective disease. Journal of Autism and Developmental Disorders, 18:593-600, 1988.
22. Finale Doshi-Velez, Yaorong Ge, and Isaac Kohane. Comorbidity clusters in autism spectrum disorders: An electronic health record time-series analysis. Pediatrics, 10.1542, 2013.
23. Finale Doshi-Velez, Byron Wallace, and Ryan Adams. Graph-sparse lda: A topic model with structured sparsity. AAAI, 2015.
24. David W Dunn, Joan K Austin, Jaroslaw Harezlak, and Walter T Ambrosius. Adhd and epilepsy in childhood. Developmental Medicine & Child Neurology, 45(01):50-54, 2003.
25. Noémie Elhadad, Shaodian Zhang, Patricia Driscoll, and Samuel Brody. Characterizing the sublanguage of online breast cancer forums for medications, symptoms, and emotions. In AMIA Annual Symposium Proceedings, volume 2014, page 516. American Medical Informatics Association, 2014.
26. Kai Fan, Marisa Eisenberg, Alison Walsh, Allison Aiello, and Katherine Heller. Hierarchical graph-coupled hmms for heterogeneous personalized health data. In ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2015.
27. Takao Furukawa, Kaoru Mori, Kazuma Arino, Kazuhiro Hayashi, and Nobuyuki Shirakawa. Identifying the evolutionary process of emerging technologies: A chronological network analysis of world wide web conference sessions. Technological Forecasting and Social Change, 91:280-294, 2015.
28. P Gail Williams, Lonnie L Sears, and AnnaMary Allard. Sleep problems in children with autism. Journal of sleep research, 13(3):265-268, 2004.
29. Gail T Gillon and Brigid C Moriarty. Childhood apraxia of speech: children at risk for persistent reading and spelling disorder. In Seminars in speech and language, volume 28, pages 48-57, 2007.
30. A Gillott, F Furniss, and A Walter. Anxiety in high-functioning children with autism. Autism, 5(3):277-286, September 2001.
31. Sylvie Goldman, Cuiling Wang, Miran W Salgado, Paul E Greene, Mimi Kim, and Isabelle Rapin. Motor stereotypies in children with autism and other developmental disorders. Developmental Medicine & Child Neurology, 51(1):30-38, 2009.
32. Sudhir Gupta, Daljeet Samra, and Sudhanshu Agrawal. Adaptive and innate immune responses in autism: rationale for therapeutic use of intravenous immunoglobulin. Journal of Clinical Immunology, 30(1):90-96, 2010.
33. Matthew D Hoffman, David M Blei, Chong Wang, and John Paisley. Stochastic variational inference. The Journal of Machine Learning Research, 14(1):1303-1347, 2013.
34. Karoly Horvath, John C Papadimitriou, Anna Rabsztyn, Cinthia Drachenberg, and J Tyson Tildon. Gastrointestinal abnormalities in children with autistic disorder. The Journal of pediatrics, 135(5):559-563, 1999.
35. V.W. Hu and M.E. Steinberg. Novel clustering of items from the autism diagnostic interview-revised to define phenotypes within autism spectrum disorders. Autism Res., 2 (2):67-77, Apr 2009.
36. Kaori Ito, Sima Ahadieh, Brian Corrigan, Jonathan French, Terence Fullerton, Thomas Tensfeldt, Alzheimer's Disease Working Group, et al. Disease progression meta-analysis model in alzheimer's disease. Alzheimer's & Dementia, 6(1):39-53, 2010.
37. Christopher H Jackson, Linda D Sharples, Simon G Thompson, Stephen W Duffy, and Elisabeth Couto. Multistate markov models for disease progression with classification error. Journal of the Royal Statistical Society: Series D (The Statistician), 52(2):193-209, 2003.
38. Mukund Jha and Noémie Elhadad. Cancer stage prediction based on patient online discourse. In Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, pages 64-71. Association for Computational Linguistics, 2010.
39. Lindsey Kent, Joanne Evans, Moli Paul, and Margo Sharp. Comorbidity of autistic spectrum disorders in children with down syndrome. Developmental Medicine & Child Neurology, 41(3):153-158, 1999.
40. I.S. Kohane, A. McMurry, G. Weber, D. MacFadden, and L. Rappaport. The co-morbidity burden of children and young adults with autism spectrum disorders. PLoS ONE, 7(4), 2012.
41. M M Konstantareas and S Homatidis. Ear infections in autistic and normal children. J Autism Dev Disord, 17(4):585-94, Dec 1987a.
42. M Mary Konstantareas and Soula Homatidis. Brief report: Ear infections in autistic and normal children. Journal of autism and developmental disorders, 17(4):585-594, 1987b.
43. A.E. Lane, R.L. Young, A.E. Baker, and M. T. Angley. Sensory processing subtypes in autism: association with adaptive behavior. J Autism Dev Disord., 40(1):112-22, Jan 2010.
44. Frédéric Laumonnier, Frédérique Bonnet-Brilhault, Marie Gomot, Romuald Blanc, Albert David, Marie-Pierre Moizard, Martine Raynaud, Nathalie Ronce, Eric Lemonnier, Patrick Calvas, et al. X-linked mental retardation and autism are associated with a mutation in the nlgn4 gene, a member of the neuroligin family. The American Journal of Human Genetics, 74(3):552-557, 2004.
45. Li-Ching Lee, Rebecca A Harrington, Brian B Louie, and Craig J Newschaffer. Children with autism: Quality of life and parental concerns. Journal of autism and developmental disorders, 38(6):1147-1160, 2008.
46. Y Li, S Swift, and A Tucker. Modelling and analysing the dynamics of disease progression from cross-sectional studies. Journal of Biomedical Informatics, 24(2), 2012.
47. Scott W. Linderman, Matthew J. Johnson, and Ryan P. Adams. Dependent multinomial models made easy: Stick breaking with the plya-gamma augmentation. In arXiv:1506.05843, 2015.
48. Yu-Ying Liu, Hiroshi Ishikawa, Mei Chen, Gadi Wollstein, Joel S Schuman, and James M Rehg. Longitudinal modeling of glaucoma progression using 2-dimensional continuous-time hidden markov model. In Medical Image Computing and Computer-Assisted Intervention-MICCAI 2013, pages 444-451. Springer, 2013.
49. Lola Luo, Dylan Small, Walter F Stewart, and Jason A Roy. Methods for estimating kidney disease stage transition probabilities using electronic medical records. EGEMS, 1 (3), 2013.
50. Carole L Marcus, Thomas G Keens, Daisy B Bautista, Walter S von Pechmann, and Sally L Davidson Ward. Obstructive sleep apnea in children with down syndrome. Pediatrics, 88(1):132-139, 1991.
51. Tomáš Mikolov. Statistical language models based on neural networks. Presentation at Google, Mountain View, 2nd April, 2012.
52. J H Miles, T N Takahashi, S Bagby, P K Sahota, D F Vaslow, C H Wang, R E Hillman, and J E Farmer. Essential versus complex autism: definition of fundamental prognostic subtypes. Am J Med Genet A., 135:171-180, June 2005.
53. X. Ming, M. Brimacombe, J. Chaaban, B. Zimmerman-Bier, and G. C. Wagner. Autism spectrum disorders: concurrent clinical disorders. Journal of Child Neurology, 23:6-13, 2008.
54. Guillermo Montes and Jill S Halterman. Bullying among children with autism and the influence of comorbidity with adhd: A population-based study. Ambulatory Pediatrics, 7 (3):253-257, 2007.
55. Isager T Mouridsen SE, Rich B. Epilepsy in disintegrative psychosis and infantile autism: a long-term validation study. . Dev Med Child Neurol, 41:110114, 1999.
56. Alistair T Pagnamenta, Elena Bacchelli, Maretha V de Jonge, Ghazala Mirza, Thomas S Scerri, Fiorella Minopoli, Andreas Chiocchetti, Kerstin U Ludwig, Per Hoffmann, Silvia Paracchini, et al. Characterization of a family with rare deletions in cntnap5 and dock4 suggests novel risk loci for autism and dyslexia. Biological psychiatry, 68(4):320-328, 2010.
57. Michael Paul. Cross-collection topic models: Automatically comparing and contrasting text. Urbana, 51:61801, 2009.
58. Michael Paul and Roxana Girju. Cross-cultural analysis of blogs and forums with mixed-collection topic models. In Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: Volume 3-Volume 3, pages 1408-1417. Association for Computational Linguistics, 2009.
59. Michael Paul, Mark Dredze, David Broniatowski, and Nicholas Generous. Worldwide influenza surveillance through twitter. In AAAI Workshop on the World Wide Web and Public Health Intelligence, 2015.
60. Nienke Peters-Scheffer, Robert Didden, Hubert Korzilius, and Peter Sturmey. A meta-analytic study on the effectiveness of comprehensive aba-based early intervention programs for children with autism spectrum disorders. Research in Autism Spectrum Disorders, 5(1):60-69, 2011.
61. Nicholas G Polson, James G Scott, and Jesse Windle. Bayesian inference for logistic models using Pólya-gamma latent variables. Journal of the American Statistical Association, 108 (504):1339-1349, 2013.
62. Teun M Post, Jan I Freijer, Joost DeJongh, and Meindert Danhof. Disease system analysis: basic disease progression models in degenerative disease. Pharmaceutical research, 22(7):1038-1049, 2005.
63. Siegfried M Pueschel. Clinical aspects of down syndrome from infancy to adulthood. American Journal of Medical Genetics, 37(S7):52-56, 1990.
64. G Ram and J Chinen. Infections and immunodeficiency in down syndrome. Clinical & Experimental Immunology, 164(1):9-16, 2011.
65. Rajesh Ranganath, Sean Gerrish, and David Blei. Black box variational inference. In Proceedings of the Seventeenth International Conference on Artificial Intelligence and Statistics, pages 814-822, 2014.
66. Peder Rasmussen, Ola Börjesson, Elisabet Wentz, and Christopher Gillberg. Autistic disorders in down syndrome: background factors and clinical correlates. Developmental Medicine & Child Neurology, 43(11):750-754, 2001.
67. AL Reyes, AJ Cash, SH Green, and IW Booth. Gastrooesophageal reflux in children with cerebral palsy. Child: care, health and development, 19(2):109-118, 1993.
68. Michal Rosen-Zvi, Thomas Griffiths, Mark Steyvers, and Padhraic Smyth. The author-topic model for authors and documents. In Proceedings of the 20th conference on Uncertainty in artificial intelligence, pages 487-494. AUAI Press, 2004.
69. Ulf Rosenhall, Viviann Nordin, Mikael Sandstrom, Gunilla Ahlsen, and Christopher Gillberg. Autism and hearing loss. J Autism Dev Disord, 29(5):349-357, October 1999.
70. James C. Ross, Peter J. Castaldi, Michael H. Cho, and Jennifer G. Dy. Dual beta process priors for latent cluster discovery in chronic obstructive pulmonary disease. In The 20th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, KDD '14, New York, NY, USA - August 24 - 27, 2014, pages 155-162, 2014.
71. R. Sacco, C. Lenti, M. Saccani, C. Paolo, B. Manzi, C. Bravaccio, and A. M. Persic. Cluster analysis of autistic patients based on principal pathogenetic components. Autism Research, 5:137-147, 2012.
72. Ardavan Saeedi and Alexandre Bouchard-Côté. Priors over recurrent continuous time processes. In Advances in Neural Information Processing Systems, pages 2052-2060, 2011.
73. Michael B Shapiro and Thomas D France. The ocular features of down's syndrome. American journal of ophthalmology, 99(6):659-663, 1985.
74. Andrew J Sharp, Heather C Mefford, Kelly Li, Carl Baker, Cindy Skinner, Roger E Stevenson, Richard J Schroer, Francesca Novara, Manuela De Gregori, Roberto Ciccone, et al. A recurrent 15q13. 3 microdeletion syndrome associated with mental retardation and seizures. Nature genetics, 40(3):322-328, 2008.
75. E H Sherr. The arx story (epilepsy, mental retardation, autism, and cerebral malformations): one gene leads to many phenotypes. Curr Opin Pediatr, 6(15):567-571, December 2003a.
76. Elliott H Sherr. The arx story (epilepsy, mental retardation, autism, and cerebral malformations): one gene leads to many phenotypes. Current opinion in pediatrics, 15(6):567-571, 2003b.
77. Sally R Shott, Aileen Joseph, and Dorsey Heithaus. Hearing loss in children with down syndrome. International journal of pediatric otorhinolaryngology, 61(3):199-205, 2001.
78. R.D. Smith. Abnormal head circumference in learning-disabled children. Dev Med Child Neurol, 23:626632, 1981.
79. Alexander E Sochaniwskyj, Ruth M Koheil, Kazek Bablich, Morris Milner, and David J Kenny. Oral motor functioning, frequency of swallowing and drooling in normal children and in children with cerebral palsy. Archives of physical medicine and rehabilitation, 67 (12):866-874, 1986.
80. Rich Stoner, Maggie L Chow, Maureen P Boyle, Susan M Sunkin, Peter R Mouton, Subhojit Roy, Anthony Wynshaw-Boris, Sophia A Colamarino, Ed S Lein, and Eric Courchesne. Patches of disorganization in the neocortex of children with autism. New England Journal of Medicine, 370(13):1209-1219, 2014.
81. Rafid Sukkar, Edward Katz, Yanwei Zhang, David Raunig, and Bradley T Wyman. Disease progression modeling using hidden markov models. In Engineering in Medicine and Biology Society (EMBC), 2012 Annual International Conference of the IEEE, pages 2845-2848. IEEE, 2012.
82. Pål Surén, Inger Johanne Bakken, Heidi Aase, Richard Chin, Nina Gunnes, Kari Kveim Lie, Per Magnus, Ted Reichborn-Kjennerud, Synnve Schjølberg, Anne-Siri Øyen, et al. Autism spectrum disorder, adhd, epilepsy, and cerebral palsy in norwegian children. Pediatrics, 130(1):e152-e158, 2012.
83. Michael E. Talkowski, Gilles Maussion, Liam Crapper, Jill A. Rosenfeld, Ian Blumenthal, Carrie Hanscom, Colby Chiang, Amelia Lindgren, Shahrin Pereira, Douglas Ruderfer, Alpha B. Diallo, Juan Pablo Lopez, Gustavo Turecki, Elizabeth S. Chen, Carolina Gigek, David J. Harris, Va Lip, Yu An, Marta Biagioli, Marcy E. MacDonald, Michael Lin, Stephen J. Haggarty, Pamela Sklar, Shaun Purcell, Manolis Kellis, Stuart Schwartz, Lisa G. Shaffer, Marvin R. Natowicz, Yiping Shen, Cynthia C. Morton, James F. Gusella, and Carl Ernst. Disruption of a large intergenic noncoding rna in subjects with neurodevelopmental disabilities. The American Journal of Human Genetics, 91:1128-1134, December 2012.
84. Stephen W Thomas, Bram Adams, Ahmed E Hassan, and Dorothea Blostein. Studying software evolution using topic models. Science of Computer Programming, 80:457-479, 2014.
85. Eeske Van Roekel, Ron HJ Scholte, and Robert Didden. Bullying among adolescents with autism spectrum disorders: Prevalence and perception. Journal of autism and developmental disorders, 40(1):63-73, 2010.
86. Chong Wang, Bo Thiesson, Christopher Meek, and David Blei. Markov topic models. In Proceedings of The Twelfth International Conference on Artificial Intelligence and Statistics, 2009.
87. Chong Wang, David Blei, and David Heckerman. Continuous time dynamic topic models. arXiv preprint arXiv:1206.3298, 2012.
88. Xiang Wang, David Sontag, and Fei Wang. Unsupervised learning of disease progression models. In Proceedings of the 20th ACM SIGKDD international conference on Knowledge discovery and data mining, pages 85-94. ACM, 2014.
89. Xuerui Wang and Andrew McCallum. Topics over time: a non-markov continuous-time model of topical trends. In Proceedings of the 12th ACM SIGKDD international conference on Knowledge discovery and data mining, pages 424-433. ACM, 2006.
90. Megan L Wier, Roxana Odouli, Cathleen K Yoshida, Judith K Grether, and Lisa A Croen. Congenital anomalies associated with autism spectrum disorders. Developmental Medicine & Child Neurology, 48(6):500-507, 2006.
91. L. D. Wiggins, D. L. Robins, L. B. Adamson, R. Bakeman, and C. C. Henrich. Support for a dimensional view of autism spectrum disorders in toddlers. J Autism Dev Disord., 42 (2):191-200, Feb 2012.
92. Kumanan Wilson and John S Brownstein. Early detection of disease outbreaks using the internet. Canadian Medical Association Journal, 180(8):829-831, 2009.
93. Jesse Windle, Nicholas G Polson, and James G Scott. Sampling Pólya-gamma random variates: alternate and approximate techniques. arXiv preprint arXiv:1405.0506, 2014.
94. L. Wing and J. Gould. Severe impairments of social interaction and associated abnormalities in children: epidemiology and classification. J Autism Dev Disord., 9(1):11-29, Mar 1979.
95. Jaewon Yang, Julian McAuley, Jure Leskovec, Paea LePendu, and Nigam Shah. Finding progression stages in time-evolving event sequences. In Proceedings of the 23rd international conference on World wide web, pages 783-794. ACM, 2014.
96. Qing Treitler Zeng. Consumer health vocabulary initiative, 2015. URL http://consumerhealthvocab.org/.
97. ChengXiang Zhai, Atulya Velivelli, and Bei Yu. A cross-collection mixture model for comparative text mining. In Proceedings of the tenth ACM SIGKDD international conference on Knowledge discovery and data mining, pages 743-748. ACM, 2004.
98. Jianwen Zhang, Yangqiu Song, Changshui Zhang, and Shixia Liu. Evolutionary hierarchical dirichlet processes for multiple correlated time-varying corpora. In Proceedings of the 16th ACM SIGKDD international conference on Knowledge discovery and data mining, pages 1079-1088. ACM, 2010.
99. Jiayu Zhou, Jun Liu, Vaibhav A Narayan, and Jieping Ye. Modeling disease progression via fused sparse group lasso. In Proceedings of the 18th ACM SIGKDD international conference on Knowledge discovery and data mining, pages 1095-1103. ACM, 2012a.
100. Jiayu Zhou, Fei Wang, Jianying Hu, and Jieping Ye. From micro to macro: data driven phenotyping by densification of longitudinal electronic medical records. In Proceedings of the 20th ACM SIGKDD international conference on Knowledge discovery and data mining, pages 135-144. ACM, 2014.
101. Mingyuan Zhou, Lingbo Li, David Dunson, and Lawrence Carin. Lognormal and gamma mixed negative binomial regression. In Proceedings of the International Conference on Machine Learning, volume 2012, page 1343, 2012b.