Computer Science International

Curriculum vitae

( last update: *th April, **** )

Name: Davide Chicco

Email: ******.******@*****.***

Website: http://www.DavideChicco.it

Mobile number: +39.348.59.04.732

Current position: Visiting scholar at University of California Irvine

Affiliation: Politecnico di Milano

Nationality: Italian

Place and date of birth: Genoa (Italy, EU), 18th October 1984

Family status: unmarried

Education:

- November 2013 -> May 2014: Visit period at University of California Irvine (CA, USA);

- March 2014: Doctoral Degree (Dottorato) in computer engineering at Politecnico di Milano university (Milan,

Italy, EU).

- July 2010: Master of Science Degree (Laurea Specialistica) in computer science at University of Genoa (Genoa,

Italy, EU). Mark: 110/110.

- July 2007: Bachelor of Science Degree (Laurea Triennale) in computer science at University of Genoa (Genoa,

Italy, EU). Mark: 104/110.

Languages: Italian (mother tongue); English (fluent); French (basic)

Current occupation: Visiting research scholar at University of California Irvine (Irvine, Orange County,

California, USA). Supervisor: Pierre Baldi.

Research interests: machine learning and data mining methods applied to bioinformatics problems; inte-

gration of web applications; deep learning methods for computational biology.

Programming and technology skills: sorted by experience: Java, C++, XML, Linux OS, Eclipse IDE,

Microsoft Visual Studio IDE, MATLAB, Jsp, REST, Torch, PostgreSQL, Apache Tomcat, Python, Perl, R.

Peer-reviewed publications: co-author of

Published:

- two book chapters [1], [2]

- eight conference proceedings papers [3], [4], [5], [6], [7], [8], [9], [10]

- one journal paper [11]

- two technical reports [12], [13]

- five posters at international conferences [14], [15], [16], [17], [18]

- three theses [19], [20], [21]

Submitted and currently under review:

- one conference paper [22]

- two journal papers [23], [24]

Teaching:

- academic years 2010/2011, 2011/2012, 2012/2013: teacher of basic computer science for the Mechanical and

Energetic Engineering Bachelor’s Degree first year students at Politecnico di Milano;

- academic years 2011/2012, 2012/2013: teacher of six lectures of the Master’s Degree course ”Bioinformatics

and Computational Biology for the Molecular Medicine” at Politecnico di Milano

- academic years 2011/2012, 2012/2013: teacher of eight lectures of the Master’s Degree course ”ICT for Health

Care and Life Science” at Politecnico di Milano

- academic year 2007/2008: teacher of the laboratory lectures of the Bachelor’s Degree course ”Basic Program-

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ming” at University of Genoa

Awards:

- Best Student Paper Award, by the International Neural Networks Society (INNS), at the 8th International

Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB2011), for the article

”Biomolecular annotation prediction through information integration” [4].

- Winner of the Bioinformatics Italian Society ”Travel Grant for Young Researchers” for attendance at Bits

2011 meeting.

- Winner of the Wikimedia Italia ”Participation Grant” for attendance to Wikimania 2011 conference.

- Winner of the ”ECCB - European Conference on Computational Biology” fellowship for attendance to

ECCB’12 conference.

- Winner of a ”PRIB & CIBB 2013 Student Grant” for the attendance to the 8th IAPR International Conference

on Pattern Recognition in Bioinformatics (PRIB 2013) and to the 10th International Meeting on Computational

Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2013).

Other scientific work experience:

- Member of the organizing committee of the NETTAB 2012 International Workshop on Integrated Bio Search

(Como, Italy, 14th - 16th November 2012).

- Desultory reviewer of papers for Data Mining and Knowledge Discovery (DAMI) journal, Sigmod Records,

Frontiers in Neuroinformatics journal.

Publications

References

[1] D. Chicco, M. Tagliasacchi, M. Masseroli, ”Genomic Annotation Prediction Based on Integrated Informa-

tion”, Computational Intelligence Methods for Bioinformatics and Biostatistics, Lecture Notes in Computer

Science Vol. 7548, Springer. 2012.

[2] P. Pinoli D. Chicco, M. Masseroli, ”Weighting Scheme Methods for Enhanced Genomic Annotation Predic-

tion”, Computational Intelligence Methods for Bioinformatics and Biostatistics, Lecture Notes in Computer

Science, Springer. 2013. In preparation.

[3] D. Chicco, M. Resta, ”An intraday trading model based on Artificial Immune Systems, Proceedings of WILF

2010 - the 20th Italian Workshop on Neural Networks. IOSPress, Amsterdam, the Netherlands, 2010.

[4] D. Chicco, M. Tagliasacchi, M. Masseroli, ”Biomolecular annotation prediction through information inte-

gration”, Proceedings of CIBB2011 - 8th International Meeting on Computational Intelligence Methods for

Bioinformatics and Biostatistics, Gargnagno sul Garda, Italy, pp. 1-9, 2011.

[5] M. Masseroli, D. Chicco, M. Tagliasacchi, ”Semantically improved genome-wide prediction of Gene Ontology

annotations”, Proceedings of ISDA2011 the 11th International Conference on Intelligent Systems Design

and Applications (ISDA). IEEE, 2011.

[6] M. Masseroli, D. Chicco, P. Pinoli, ”Probabilistic Latent Semantic Analysis for prediction of Gene Ontol-

ogy annotations”, Proceedings of IJCNN - The 2012 International Joint Conference on Neural Networks

(IJCNN), IEEE.

[7] P. Pinoli, D. Chicco, M. Masseroli, ”Improved Biomolecular Annotation Prediction through Weighting

Scheme Methods”, Proceedings of CIBB2013 - 10th International Meeting on Computational Intelligence

Methods for Bioinformatics and Biostatistics, Nice, France, pp. 1-9, 2013.

[8] P. Pinoli, D. Chicco, M. Masseroli, ”Enhanced Probabilistic Latent Semantic Analysis with Weighting

Schemes to Predict Genomic Annotations”, Proceedings of IEEE BIBE 2013 the 13rd IEEE International

Conference on Bioinformatics and Bioengineering, Chania, Crete, Greece, 2013.

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[9] D. Chicco, M. Masseroli, ”A Discrete Optimization Approach for SVD Best Truncation Choice based on

ROC Curves”, Proceedings of IEEE BIBE 2013 the 13rd IEEE International Conference on Bioinformatics

and Bioengineering, Chania, Crete, Greece, 2013.

[10] P. Pinoli, D. Chicco, M. Masseroli, ”Latent Dirichlet Allocation based on Gibbs Sampling for Gene Function

Prediction”, Proceedings of IEEE CIBCB 2014, Conference on Computational Intelligence in Bioinformatics

and Computational Biology, in press.

[11] P. Pinoli, D. Chicco, M. Masseroli, ”Computational Algorithms to Predict Gene Ontology Annotations”,

BMC Bioinformatics. SUBMITTED.

[12] D. Chicco, ”Support Vector Machines in Bioinformatics: a Survey”, Technical Report TR-2012/01, Dipar-

timento di Elettronica e Informazione, Politecnico di Milano, Milan, Italy, 2012.

[13] D. Chicco, ”Integration of Bioinformatics Web Services through the Search Computing Technology”, Tech-

nical Report TR-2012/02, Dipartimento di Elettronica e Informazione, Politecnico di Milano, Milan, Italy,

2012.

[14] D. Chicco, M. Masseroli, M. Tagliasacchi, ”Improved Singular Value Decomposition methods for Biomolec-

ular Annotation Prediction, Proceedings of Bits2011 the 8th Annual Meeting of the Bioinformatics Italian

Society, Pisa, Italy, 2011.

[15] D. Chicco, M. Masseroli, ”Truncated SVD best rank choice through ROC curves for genomic annotation

prediction”, Proceedings of Bits2012 the 9th Annual Meeting of the Bioinformatics Italian Society, Catania,

Italy, 2012.

[16] D. Chicco, M. Masseroli, ”Genome-Wide Annotation Prediction with SVD Truncation based on ROC

Analysis, Proceedings of ISCB ESCS 2012 the 2nd International Society for Computational Biology European

Student Council Symposium, Basel, Switzerland, 2012.

[17] M. Masseroli, M. Picozzi, D. Ghisalberti, D. Chicco, ”Ranking-Aware Integration and Explorative Search

of Distributed Bio-Data”, Proceedings of Nettab2012 International Conference on Integrated Bio-Search,

Como, Italy, 2012.

[18] D. Chicco, M. Masseroli, ”Integration of a gene similarity service for explorative search computing”, Pro-

ceedings of Bits2013 the 10th Annual Meeting of the Bioinformatics Italian Society, Udine, Italy, 2013.

[19] D. Chicco, ”Middleware per la bioinformatica: implementazione dellAlgoritmo dei Distanti per il clustering

dei dati nellambiente OpenAdap.net”, Bachelor’s of Science Degree in computer science, University of Genoa,

July 2007.

[20] D. Chicco, ”Elaborazione di dati bioinformatici attraverso luso di Particle Swarm Optimization”, Master’s

of Science Degree in computer science, University of Genoa, July 2010.

[21] D. Chicco, ”Computational Prediction of Gene Functions through Machine Learning methods and Multiple

Validation Procedures”, PhD in computer engineering, Politecnico di Milano, March 2014.

[22] D. Chicco, E. Cicieri, M. Masseroli, ”Correlation of Gene Function Annotation Lists through Enhanced

Spearman and Kendall Measures”, Proceedings of CIBB2014 - 11th International Meeting on Computational

Intelligence Methods for Bioinformatics and Biostatistics. SUBMITTED.

[23] D. Chicco, M. Masseroli, ”Software Suite for Gene and Protein Annotation Prediction and Similar-

ity Search”, IEEE/ACM Transactions on Computational Biology and Bioinformatics - Special issue on

databases and software. SUBMITTED.

[24] D. Chicco, M. Masseroli, ”Prediction and Prioritization of Gene Functions through Machine Learning

Methods”, IEEE/ACM Transactions on Computational Biology and Bioinformatics. SUBMITTED.

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