Special session sponsored by

SIG on Bioinformatics of the International Neural Network Society (INNS)


Soft Computing tools for Bioinformatics


International Joint Conference on Neural Networks (IJCNN 2009)

Westin PeachTree Hotel, Atlanta, Georgia, USA, June 14-19 2009 




Description and Scope:

The body of information surrounding molecular and genomic experiments and clinical investigations is rapidly growing as the magnitude and rate of applications involving large-scale high-throughput technologies are ever-increasing. Bioinformatic data mining efforts now range from more recent methods including miRNA target identification and protein structure prediction to classical methods such as ANN and RBFN classification of DNA microarray gene expression data. Data fusion and integration are also gaining considerable attention for merging signals, features, images, and text data from multiple sensors together in order to understand influences of data components on early detection and diagnosis of disease. Altogether, bioinformatics has become a very promising multidisciplinary research area in the life sciences because results provide new insights for interpretation and establish new leads for deeper understanding. Each year there are numerous Soft Computing and Machine Learning algorithms introduced providing new examples of application in related fields (clustering, feature selection, text mining, signal and image processing, data visualization, etc.). This session will take stock in new soft computing methods for bioinformatic data mining in general, and Neural Network methods in particular.


We welcome papers which present novel algorithms or refined classical methods for the analysis of high dimensional bioinformatic data sets. The range of topics includes but is not limited to:

*       Data integration and fusion
*       Ensemble techniques
*       Biological sequence identification
*       DNA/CGH/SNP/miRNA arrays
*       Gene regulatory and ontology networks
*       Protein-protein, protein-small molecule interactions
*       Protein structure prediction
*       Cellular metabolism and signaling
*       Pharmacogenomics and pharmacodynamics
*       Metabolic pathways
*       Signal processing
*       Unsupervised and supervised classification
*       Imaging/data visualization
*       Text mining methods
*       Biomarker selection


Alexandru Floares (1), Francesco Masulli (2,3)

(1) Department of Artificial Intelligence
Oncological Institute Cluj-Napoca
400015 Str. Republicii, Nr. 34-36, Cluj-Napoca Romania
E-mail: alexandru.floares <at> iocn.ro

(2) DISI Dept. Computer and Information Sciences
University of Genova
Via Dodecaneso 35, 16146 Genoa, Italy
E-mail: masulli <at> disi.unige.it

(3) Sbarro Institute for Cancer Research and Molecular Medicine,
Temple University, 1900 N 12th Street Philadelphia, PA 19122, USA.

Important deadlines:

As soon as possibile
Inform by email the SS organizers of your willness to submit a paper

Jannuary 5, 2009

Paper submission deadline  (&)

Jannuary 30, 2009

Author notification of acceptance or rejection

March 10, 2009

Deadline for final paper re-submission (&&)

(&) Paper submission (deadline Jan 5, 2009):

At http://cnd.memphis.edu/ijcnn2009/submission.html you'll find the Instruction for Authors and the link to the IJCNN 2009 submission site.  IMPORTANT: While submitting,  select  Main research topic as "S04. SC Tools for Bioinformatics (Chairs: Francesco Masulli & Alexandru Floares)" only.  Don't select any Additional rearch topics.

After uploaded your paper on the IJCNN 2009 submission site, send  by email to the special session organizers  a copy of your paper.   In the Subject of the email please specify: "Paper submitted to SS on Bioinformatics IJCNN09".

(&&) Final Paper re-submission (deadline March 10, 2009):

After re-uploaded your paper on the IJCNN 2009 submission site,  send  by email to the special session organizers a copy of your revised paper and a letter indicating in detail all  changes made.  In the Subject of the email please specify: "Paper submitted to SS on Bioinformatics IJCNN09 (revised)".

Final Program

Session S04: SC Tools for Bioinformatics
Thursday, June 18, 9:30AM-11:30AM, Room: A, Chair: Alexandru Floares and Francesco Masulli

9:30AM   Inference of Genetic Networks using Linear Programming Machines: Application of a Priori Knowledge [#152]

Shuhei Kimura, Yuichi Shiraishi and Mariko Hatakeyama

Tottori University, Japan; Advanced Science Institute, RIKEN, Japan
9:50AM   A Neural Networks Algorithm for Inferring Drug Gene Regulatory Networks From Microarray Time-Series With Missing Transcription Factors Information [#681]

Alexandru Floares

Oncological Institute Cluj-Napoca, Romania
10:10AM   Searching for MicroRNA Prostate Cancer Target Genes [#627]

Francesco Masulli, Alessandro Parini, Stefano Rovetta and Giuseppe Russo

University of Genova, Italy, and Temple University, Philadelphia, USA, Italy; University of Genova, Italy, Italy; Temple University, Philadelphia, USA, and University of Genova, Italy, United States
10:30AM   Investigation into Effectiveness of Rough Sets in Prediction of Enzyme and Protein Structure Classes [#176]

Chris Newby, Yingjie Yang and Huseyin Seker

Leicester University, United Kingdom; De Montfort University, United Kingdom
10:50AM   Neural Network Model for Integration and Visualization of Introgressed Genome and Metabolite Data [#629]

Georgina Stegmayer, Diego Milone, Laura Kameneztky, Mariana Lopez and Fernando Carrari

CIDISI, CONICET, Argentina; sinc(i), FICH-UNL, CONICET, Argentina; GEFEIA, INTA-IB, CONICET, Argentina
11:10AM   Global Optimization, Meta Clustering and Consensus Clustering for Class Prediction of a Biological Dataset [#302]

Ida Bifulco, Carmine Fedullo, Francesco Napolitano, Giancarlo Raiconi and Roberto Tagliaferri

Dipartimento di Matematica e Informatica (DMI), University of Salerno, Italy