Protein Interaction Abstract Relevance Evaluation (PIARE) service, was created to implement the binary classifier we produced for the Protein-Protein Interaction Article Classification Task in Biocreative II and Biocreative II.5. Supplementary materials for our Biocreative III paper are available as a zip file with instructions.
Biomedical Literature Mining
A. Abi-Haidar, J. Kaur, A. Maguitman, P. Radivojac, A. Retchsteiner, K. Verspoor, Z. Wang, and L.M. Rocha . “
Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks“. Genome Biology. 9(Suppl 2):S11
A. Kolchinsky, A. Abi-Haidar, J. Kaur, A.A. Hamed and L.M. Rocha . “
Classification of protein-protein interaction full-text documents using text and citation network features.” IEEE/ACM Transactions On Computational Biology And Bioinformatics, 7(3):400-411. DOI: doi.ieeecomputersociety.org/10.1109/TCBB.2010.55
A. Lourenço, M. Conover, A. Wong, A. Nematzadeh, F. Pan, H. Shatkay, and L.M. Rocha .”
A Linear Classifier Based on Entity Recognition Tools and a Statistical Approach to Method Extraction in the Protein-Protein Interaction Literature“. BMC Bioinformatics. 12(Suppl 8):S12. DOI: 10.1186/1471-2105-12-S8-S12.
School of Informatics and Computing
My web site and Research Lab (CASCI). Bio
Luis M. Rocha is Professor of Informatics in the School of Informatics, Computing, and Engineering at Indiana University, Bloomington, where he is director of the NSF-NRT Interdisciplinary Training Program in Complex Networks and Systems, director of the Complex Networks & Systems track of the Informatics PhD Program, member of the Indiana University Network Science Institute, and core faculty of the Cognitive Science Program. Dr. Rocha is a Fulbright Scholar and is Principal Investigator at the Instituto Gulbenkian da Ciencia, Portugal, and Visiting Professor of the Neuroscience Program, at the Champalimaud Foundation in Portugal, and the Center for Theoretical Physics at the Aix-Marseille University, France. His research is on complex networks & systems, Computational & Systems Biology, and Computational Intelligence and he is the Principal Investigator of the Complex Adaptive Systems & Computational Intelligence lab (CASCI). He received his Ph.D in Systems Science in 1997 from the State University of New York at Binghamton. From 1998 to 2004 he was a permanent staff scientist at the Los Alamos National Laboratory, where he founded and led a Complex Systems Modeling Team during 1998-2002, and was part of the Santa Fe Institute research community. He has organized major conferences such as the Tenth International Conference on the Simulation and Synthesis of Living Systems (Alife X) and the Ninth European Conference on Artificial Life (ECAL 2007). He has published many articles in scientific and technology journals, and has been the recipient of several scholarships and awards. At Indiana University, he has received the Indiana University, School of Informatics & Computing, Trustees Award for Teaching Excellence in 2006 and 2015 after developing the complex systems training program and syllabi for several courses. Additional information about Prof. Rocha’s research, academic and personal activities is available on his website. Contact Information:
In The USA:
Center for Complex Networks and Systems Research
School of Informatics & Computing
Indiana University, 919 E. 10th St
Bloomington IN, 47408, USA
Instituto Gulbenkian de Ciência
Rua da Quinta Grande, 6
Apartado 14, P-2781-901 Oeiras, Portugal
Complex Adaptive Systems and Computational Intelligence
Complex Adaptive Systems and Computational Intelligence (CASCI) group at Indiana University and the Instituto Gulbenkian de Ciencia works on and their applications to informatics, biology, health, and social systems. We are particularly interested in the informational properties of natural and artificial systems which enable them to adapt and evolve. This means both understanding how information is fundamental for controlling the behavior and evolutionary capabilities of complex systems, as well as abstracting principles from natural systems to produce adaptive information technology. complex networks & systems
are on research projects complex networks & systems, computational and systems biology, and computational intelligence; all our publications are available online as are news about our group. Additional information available and on Luis Rocha’s Website our group page at the Instituto Gulbenkian de Ciencia.
current roster and information on how to join our group. As a group, we are seriously interconnected with other research groups and networks: The Center for Complex Networks and Systems (CNets), the Indiana University Network Science Institute, the Cognitive Science Program, the FLAD Computational Biology Collaboratorium, the Instituto Gulbenkian de Ciência, and the Champalimaud Neuroscience Program.
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