Tag Archives: CASCI

NIH Project to study Drug-Drug Interaction


Prof. Luis Rocha from CNETS at IU Bloomington, Prof. Lang Li from IUPUI Medical School, and Prof. Hagit Shatkay from the University of Delaware have been awarded a four-year, $1.7M grant from NIH/NLM to study the large-scale extraction of drug-Interaction from medical text. Drug-drug interaction (DDI) leads to adverse drug reactions, emergency room visits and hospitalization, thus posing a major challenge to public health. To circumvent risk to patients, and to expedite biomedical research, both clinicians and biologists must have access to all available knowledge about potential DDI, and understand both causes and consequences of such interactions. However, mere identification of interactions does not directly support such understanding, as evidence for DDI varies broadly, from reports of molecular interactions in basic-science journals, to clinical descriptions of adverse-effects in a myriad of medical publications. This project will develop tools that focus directly on large-scale identification and gathering of various types of reliable experimental evidence of DDI from diverse sources. The successful completion of the project will provide clinicians and biologists with substantiated knowledge about drug interactions and with informatics tools to obtain such information on a large-scale, laying the basis for preventing adverse drug reactions and for exploring alternative treatments.

PIARE (Protein Interaction Abstract Relevance Evaluator)

Research | People | Academics | News and Meetings | Publications-online | Media Mentions | Relevant Conferences

The 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.

Literature Mining
Biomedical Literature Mining

Relevant Publications:

A. Abi-Haidar, J. Kaur, A. Maguitman, P. Radivojac, A. Retchsteiner, K. Verspoor, Z. Wang, and L.M. Rocha [2008]. “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 [2010]. “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 [2011].”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.

Luis Rocha

Luis Rocha
Luis Rocha

Professor
School of Informatics and Computing
Indiana University

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

In Portugal:
Instituto Gulbenkian de Ciência
Rua da Quinta Grande, 6
Apartado 14, P-2781-901 Oeiras, Portugal

Course and research-related blogs

News


CASCI Research| People | Academics | News and Meetings | Publications-online | Media Mentions | Relevant Conferences


New CASCI Alumnus in 2015

Congratulations to Artemy Kolchinsky a brand new PhD in 2015 in the Complex Systems track of the Informatics PhD Program. Artemy’s PhD Dissertation is entittled “Measuring Scales: Integration and Modularity in Complex Systems“.

Artemy Kolchinsky Dissertation Defense
Artemy Kolchinsky Dissertation Defense. April 2015.

New papers on Complex Networks

Network Science Journal
Network Science

Read new papers from CASCI on developing the mathematical toolbox available to deal with computing distances on weighted graphs, applying distance closures for computational fact checking, and computing multi-scale integration in brain networks:

T. Simas and L.M. Rocha [2015].”Distance Closures on Complex Networks”. Network Science, doi:10.1017/nws.2015.11.

G.L. Ciampaglia, P. Shiralkar, L.M. Rocha, J. Bollen, F. Menczer, A. Flammini [2015]. “Computational fact checking from knowledge networks.” PLoS One. In Press. arXiv:1501.03471.

A. Kolchinsky, M. P. Van Den Heuvel, A. Griffa, P. Hagmann, L.M. Rocha, O. Sporns, J. Goni [2014]. “Multi-scale Integration and Predictability in Resting State Brain Activity”. Frontiers in Neuroinformatics, 8:66. doi: 10.3389/fninf.2014.00066.

NIH/NLM Project to study Drug-Drug Interaction


Prof. Luis Rocha from CNETS at IU Bloomington, Prof. Lang Li from IUPUI Medical School, and Prof. Hagit Shatkay from the University of Delaware have been awarded a four-year, $1.7M grant from NIH to study the large-scale extraction of drug-Interaction from medical text. Drug-drug interaction (DDI) leads to adverse drug reactions, emergency room visits and hospitalization, thus posing a major challenge to public health. To circumvent risk to patients, and to expedite biomedical research, both clinicians and biologists must have access to all available knowledge about potential DDI, and understand both causes and consequences of such interactions. However, mere identification of interactions does not directly support such understanding, as evidence for DDI varies broadly, from reports of molecular interactions in basic-science journals, to clinical descriptions of adverse-effects in a myriad of medical publications. This project will develop tools that focus directly on large-scale identification and gathering of various types of reliable experimental evidence of DDI from diverse sources. The successful completion of the project will provide clinicians and biologists with substantiated knowledge about drug interactions and with informatics tools to obtain such information on a large-scale, laying the basis for preventing adverse drug reactions and for exploring alternative treatments.

Persistent Systems Project


A new grant to analyze social media for health risks and adverse drug reactions from Persistent Systems, was awarded to CASCI.

Canalization and Control in Automata Networks

Dynamical Modularity
Dynamical Modularity

Read our latest paper titled Canalization and Control in Automata Networks: Body Segmentation in Drosophila melanogaster in PLoS ONE. Authors Manuel Marques-Pita & Luis Rocha ask, How do cells and tissues ‘compute’? Schema redescription is presented as a methodology to characterize canalization in automata networks used to model biochemical regulation and signalling. Canalization becomes synonymous with redundancy present in the logic of automata. This results in straightforward measures to quantify canalization in an automaton (micro-level), which is in turn integrated into a highly scalable framework to characterize the collective dynamics of large-scale automata networks (macro-level). Several new results ensue from this methodology developed as part of the CASCI collective dynamics project: uncovering of dynamical modularity (modules in the dynamics rather than in the structure of networks), identification of minimal conditions and critical nodes to control the convergence to attractors, simulation of dynamical behaviour from incomplete information about initial conditions, and measures of macro-level canalization and robustness to perturbations. The methodology is applicable to any complex network that can be modelled using automata, but this work focuses on biochemical regulation and signalling, with a well-known model of the intra- and inter cellular genetic regulation of body segmentation in Drosophila melanogaster.

New Indiana University Collaborative Research Grant 2013


The project “Social SLAM: Creating Dynamical Socio-Environmental Models for Mobile Robots”, a collaboration between CASCI and Selma Sabanovic, Matt Francisco, and Alin Cosmanescu, has received an IUCRG grant for 2013-2014 from the Office of the Vice President for Research at Indiana University.

Highly accessed paper in BMC Bioinformatics


The pharmacokinetics ontology and corpus for text mining developed in collaboration with Li’s lab at IUPUI, part of our Biomedical Literature Mining work, has been reported in BMC Bioinformatics where it has become a Highly Accessed paper:

Wu, Hengyi, S. Karnik, A. Subhadarshini, Z. Wang, S. Philips, X. Han, C. Chiang, L. Liu, M. Boustani, L.M. Rocha, S.K. Quinney, D.A. Flockhart and L. Li [2013]. “An Integrated Pharmacokinetics Ontology and Corpus for Text Mining”. BMC Bioinformatics. 14:35. DOI:10.1186/1471-2105-14-35.

CareerBuilder.com Project


A new grant to develop recommendation systems for CareerBuilder.com, which is the largest online job site in the U.S., was awarded to CASCI.

New CASCI Alumnus in 2013

Congratulations to Zhiping Wang a brand new PhD in 2013 in the Computer Science Program. Zhiping’s PhD Dissertation is entittled ” Biomedical Literature Mining for Pharmacokinetics Numerical Parameter Collection”. He has accepted a posdoctoral position at the Lang Li lab at the IUPUI School of Medicine.

Zhiping Wang Dissertation Defense
Zhiping Wang Dissertation Defense. December 2012.

IARPA contract to study new ways to forecast critical societal events

University and industry scientists are determining how to forecast significant societal events, ranging from violent protests to nationwide credit-rate crashes, by analyzing the billions of pieces of information in the ocean of public communications, such as tweets, web queries, oil prices, and daily stock market activity.


“We are automating the generation of alerts, so that intelligence analysts can focus on interpreting the discoveries rather than on the mechanics of integrating information,” said Naren Ramakrishnan, the Thomas L. Phillips Professor of Engineering in the computer science department at Virginia Tech. He is leading the team of computer scientists and subject-matter experts from Virginia Tech, the University of Maryland, Cornell University, Children’s Hospital of Boston, San Diego State University, University of California at San Diego, and Indiana University, and from the companies, CACI International Inc., and Basis Technology.

CNetS Professors Bollen and Rocha from the School of Informatics and Computing at Indiana University are members of this project. Prof. Bollen, has devised a way to evaluate the tone of tweets – calm, alert, vital, etc. — to predict stock market trends. Prof. Rocha, has developed bio-inspired methods to predict associations in biochemical, social, and knowledge networks, including web and e-mail systems.

Additional details: Researchers study new ways to forecast critical societal events.

CASCI student receives Fellowship from the Biocomplexity Institute – Academic year 2012/2013

Artemy Kolchinsky received the Eli Lilly Graduate Fellowship from the Biocomplexity Institute. This fellowship is offered by the Lilly Foundation to talented students with interdisciplinary interests in the area of Biocomplexity.

New CASCI Alumni in 2012

Congratulations to Tiago Simas a brand new PhD in 2012 in the Cognitive Science Program. Tiago’s PhD Dissertation is entittled “Stochastic Models And Transitivity In Complex Networks”. He has accepted a posdoctoral position at the Brain Mapping Unit of the University of Cambridge. Congratulations also to Thomas Parmer who graduated from a dual degree, BS in cognitive science and BA in biophysics, through the the Individualized Major Program at Indiana University. Thomas’ undergraduate thesis is entitled: “Inducing Apoptosis: The Study of a Random Boolean Network Modelling Survival Signalling in T-LGL Leukemia

Thomas Graduates
Thomas Parmer Graduation. May 2012.

3 CASCI students receive IGERT Associate Fellowships – Summer 2012

Artemy Kolchinsky, Santosh Manicka, and Alexander Gates have been accepted as associates of the NSF-sponsored IGERT on “The dynamics of brain-body-environment systems in behavior and cognition“. Associate status comes with a generous $5000 summer stipend from the School of Informatics and Computing.

New CASCI Alumni in 2011

Congratulations to Alaa Abi-Haidar and Marcio Mourao, brand new PhDs in 2011. They are also the first PhD students out of the Complex Systems track of the PhD program in Informatics at Indiana University. Al’s PhD Dissertation is entittled “An adaptive document classifier inspired by T-Cell cross-regulation in the immune system“; Marcio’s dissertation is entitled “Reverse engineering the mechanisms and dynamical behavior of complex biochemical pathways“.

Al gets Hooded
Al Hooded by Luis (and Jacob by Fil). May 2011.

2 CASCI students receive IGERT Associate Fellowships

Artemy Kolchinsky and Santosh Manicka have been accepted as associates of the NSF-sponsored IGERT on “The dynamics of brain-body-environment systems in behavior and cognition“. Associate status comes with a generous $5000 summer stipend from the School of Informatics and Computing.

New IUCRG grant Received

In collaboration with Lang Li and Jon Duke at IUPUI Medical School, our proposal “Drug-Drug Interaction Prediction from Large-scale Mining of Literature and Patient Records” has been funded by Indiana University Collaborative Research Grants 2011. A summary of our research in this area is available.


In the Spring of 2012, our group meets regularly every Thursday 1-2:30pm.


All CASCI News Posts

CASCI

Complex Adaptive Systems and Computational Intelligence

The Complex Adaptive Systems and Computational Intelligence (CASCI) group at Indiana University and the Instituto Gulbenkian de Ciencia works on complex networks & systems 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.

Our research projects are on 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 on Luis Rocha’s Website and our group page at the Instituto Gulbenkian de Ciencia.

See our 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.

You are welcome to join our mailing list CASCI-L by sending an email message to list@list.indiana.edu from the address you want to subscribe to the list, with subject line: subscribe CASCI-L Firstname Lastname (leave the message body blank.) More detailed instructions are available.