Papers

• A review of causal inference for biomedical informatics
  Samantha Kleinberg and George Hripcsak.
  Journal of Biomedical Informatics (JBI), 2011 (in press)
  [pdf] [ScienceDirect]
• A Logic for Causal Inference in Time Series with Discrete and Continuous Variables
  Samantha Kleinberg.
  International Joint Conference on Artificial Intelligence (IJCAI), 2011
  [pdf]
• Multiple Testing of Causal Hypotheses
  Samantha Kleinberg and Bud Mishra.
  Causality in the Sciences, Oxford University Press 2011
  (Phyllis McKay Illari, Federica Russo & Jon Williamson eds.)
• The Temporal Logic of Token Causes
  Samantha Kleinberg and Bud Mishra.
  Principles of Knowledge Representation and Reasoning (KR), 2010
  Extended version: CIMS Technical Report TR2010-926
  [extended pdf]
• Predicting malaria interactome classifications from time-course transcriptomic data along the intraerythrocytic developmental cycle
  Antonina Mitrofanova, Samantha Kleinberg, Jane Carlton, Simon Kasif, and Bud Mishra.
  Artificial Intelligence in Medicine 49(3):167-176, 2010
  [ScienceDirect] [bibtex]
• Metamorphosis: The Coming Transformation of Translational Systems Biology
  Samantha Kleinberg and Bud Mishra.
  ACM Queue, 2009
  [pdf] [bibtex]
• The Temporal Logic of Causal Structures
  Samantha Kleinberg and Bud Mishra.
  Uncertainty in Artificial Intelligence (UAI), 2009
  [pdf] [bibtex] [Supplementary material]
• Systems Biology via Redescription and Ontologies (III): Protein Classification using Malaria Parasite's Temporal Transcriptomic Profiles
  Antonina Mitrofanova, Samantha Kleinberg, Jane Carlton, Simon Kasif, and Bud Mishra
  IEEE BIBM 2008
  [bibtex]
• Systems Biology via Redescription and Ontologies (II): A Tool for Discovery in Complex Systems
  Samantha Kleinberg, Marco Antoniotti, Satish Tadepalli, Naren Ramakrishnan and Bud Mishra
  Unifying Themes in Complex Systems, Volume VI: Proceedings of the Sixth International Conference on Complex Systems, 2008
  [pdf]
• Systems Biology via Redescription and Ontologies (I): finding phase changes with applications to malaria temporal data
  Samantha Kleinberg, Kevin Casey, and Bud Mishra
  Systems and Synthetic Biology (SSB) 1(4):197-205, December 2007
  [pdf] [Springer] [bibtex]
• Modal Logic, Temporal Models and Neural Circuits: What Connects Them
  Samantha Kleinberg, Marco Antoniotti, Naren Ramakrishnan, and Bud Mishra
  CIMS Technical Report TR2007-907
  [pdf]
• Systems Biology via Redescription and Ontologies: Untangling the Malaria Parasite Life Cycle
  Samantha Kleinberg, Kevin Casey, and Bud Mishra
  LSMS 07, Shanghai, China, September 14-17, 2007
• Remembrance of Experiments Past: A Redescription Based Tool for Discovery in Complex System
  Samantha Kleinberg, Marco Antoniotti, Satish Tadepalli, Naren Ramakrishnan and Bud Mishra
  Interational Conference on Complex Systems, Quincy, MA, June 2006

Abstracts and Posters

• "Understanding variable representation for causal inference in EHRs" (Samantha Kleinberg and George Hripcsak) AMIA TBI 2011, San Francisco.
• "A causal understanding of electronic health records" (Samantha Kleinberg) Causality in the Biomedical and Social Sciences, Rotterdam, NL 2010
• "Multiple Testing of Causal Hypotheses"(Samantha Kleinberg and Bud Mishra) CAPITS 2008 Causality Study Fortnight, Canterbury, UK, September 8-19.
• "PSST: A web-based system for tracking political statements" (Samantha Kleinberg and Bud Mishra) WWW 2008 Beijing, China.
• "Logic in the Time of Malaria: Segmenting Time Course Data to Understand the Plasmodium Falciparum Life Cycle" (Samantha Kleinberg, Kevin Casey, and Bud Mishra), APBC 08, Kyoto, Japan, January 14-17, 2008.
• "CLARITY: Algorithms for Semantic Comparison of Time-course Transcriptomic Data," (Samantha Kleinberg and Bud Mishra), International Symposium on Computational Biology & Bioinformatics: ISBB 06, Bhubaneswar, India, December 15-17, 2006.