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The CA3 group is composed of a research and development team and a group of qualified scientific advisors directly involved in R&D projects where CA3 is a partner.

We also have a variable number of visiting scientists and collaborators working with us. The former member section has previous group members.

José Manuel Fonseca (Ph.D.) - Senior Research team
Research Interests
My research interests include Image Processing, decision support systems and healthcare information systems.
Current Projects
  • SINAIS - Sistema de apoio à navegação baseado em sinais AIS
  • ARINCA - Armazém Seguro de Cartões de Identificação Personalizados
  • BioPattern - Computational Intelligence for Biopattern analysis in Support of eHealthcare
  • DRUSAS – Automatic detection of Drusen deposits on retina images
  • COSIS - Coimbra Observatory: Solar Information System
Publications
Capítulos de livros publicados
  • AMora, André D; Fonseca, José M; Vieira, Pedro M. 2012. Variability and Repeatability Tests of ARMD Assessment Using the AD3RI Tool. In Technological Innovation for Value Creation, ed. Luis M. Camarinha-Matos, Ehsan Shahamatnia, Gonçalo Nunes, 583 - 590. ISBN: 978-3-642-28254-6. Berlin, Heidelberg: Springer Berlin Heidelberg.
    doi: 10.1007/978-3-642-28255-3_65
  • Almeida, Graça; Melicio, Fernando; Chastre, Carlos; Fonseca, José. 2011. Displacement Measurements with ARPS in T-Beams Load Tests. In Technological Innovation for Sustainability, ed. Luis M. Camarinha-Matos, 286 - 293. ISBN: 978-3-642-19169-5. Berlin, Heidelberg: Springer Berlin Heidelberg.
    doi: 10.1007/978-3-642-19170-1_31
  • Fernandes, Ana S; Bacciu, Davide; Jarman, Ian H; Etchells, Terence A; Fonseca, José M; Lisboa, Paulo J. G. 2010. Different Methodologies for Patient Stratification Using Survival Data. In Computational Intelligence Methods for Bioinformatics and Biostatistics, ed. Francesco MasulliLeif E. PetersonRoberto Tagliaferri, 276 - 290. ISBN: 978-3-642-14570-4. Berlin, Heidelberg: Springer Berlin Heidelberg.
    doi: 10.1007/978-3-642-14571-1_21
  • Fernandes, Ana S; Alves, Pedro; Jarman, Ian H; Etchells, Terence A; Fonseca, José M; Lisboa, Paulo J. G. 2010. A Clinical Decision Support System for Breast Cancer Patients. In Emerging Trends in Technological Innovation, ed. Luis M. Camarinha-MatosPedro PereiraLuis Ribeiro, 122 - 129. ISBN: 978-3-642-11627-8. Berlin, Heidelberg: Springer Berlin Heidelberg.
    doi: 10.1007/978-3-642-11628-5_13
  • Mora, André; Vieira, Pedro; Fonseca, José. 2010. Advances in Image Processing Techniques for Drusens Detection and Quantification in Fundus Images. In Emerging Trends in Technological Innovation, ed. Luis M. Camarinha-MatosPedro PereiraLuis Ribeiro, 299 - 307. ISBN: 978-3-642-11627-8. Berlin, Heidelberg: Springer Berlin Heidelberg.
    doi: 10.1007/978-3-642-11628-5_32
  • Mora, A.; Fonseca, J.; Veira, P.. 2009. Retina Image Gradings' Comparison by Weighted Matching Analysis. In World Congress on Medical Physics and Biomedical Engineering, September 7 - 12, 2009, Munich, Germany, ed. Olaf DösselWolfgang C. Schlegel, 296 - 299. ISBN: 978-3-642-03890-7. Berlin, Heidelberg: Springer Berlin Heidelberg.
    doi: 10.1007/978-3-642-03891-4_79
  • Fernandes, Ana S; Jarman, Ian H; Etchells, Terence A; Fonseca, José M; Biganzoli, Elia; Bajdik, Chris; Lisboa, Paulo J. G. 2009. Stratification Methodologies for Neural Networks Models of Survival. In Bio-Inspired Systems: Computational and Ambient Intelligence, ed. Joan CabestanyFrancisco SandovalAlberto PrietoJuan M. Corchado, 989 - 996. ISBN: 978-3-642-02477-1. Berlin, Heidelberg: Springer Berlin Heidelberg.
    doi: 10.1007/978-3-642-02478-8_124
  • Etchells, Terence A; Fernandes, Ana S; Jarman, Ian H; Fonseca, José M; Lisboa, Paulo J. G. 2008. Stratification of Severity of Illness Indices: A Case Study for Breast Cancer Prognosis. In Knowledge-Based Intelligent Information and Engineering Systems, ed. Ignac LovrekRobert J. HowlettLakhmi C. Jain, 214 - 221. ISBN: 978-3-540-85564-4. Berlin, Heidelberg: Springer Berlin Heidelberg.
    doi: 10.1007/978-3-540-85565-1_27
  • Fonseca, José M; Mora, André D; Barroso, Pedro. 2006. The Web and the New Generation of Medical Information Systems. In Outcome Prediction in Cancer, 391 - 414. . UK: Elsevier.
  • Fonseca, Jose M; Oliveira, Eugénio; Steiger-Garção, Adolfo. 1997. Multi-agent negotiation algorithms for resources cost estimation: A case study. In Progress in Artificial Intelligence, ed. Ernesto CoastaAmilcar Cardoso, 195 - 206. ISBN: 3-540-63586-6. Berlin/Heidelberg: Springer-Verlag.
    doi: 10.1007/BFb0023922
Artigos em revistas com arbitragem científica
  • Shahamatnia, Ehsan; Dorotovic, Ivan; Ribeiro, Rita A; Fonseca, José M. 2012. "Towards an automatic sunspot tracking: Swarm intelligence and snake model hybrid", Acta Futura , 5: 153 - 161.
    doi: 10.2420/AF05.2012.153
  • Martins, Leonardo; Mäkelä, Jarno; Häkkinen, Antti; Kandhavelu, Meenakshisundaram; Yli-Harja, Olli; Fonseca, José M; Ribeiro, Andre S. 2012. "Dynamics of transcription of closely spaced promoters in Escherichia coli, one event at a time", Journal of Theoretical Biology 301, 5: 83 - 94.
    doi: 10.1016/j.jtbi.2012.02.015
  • Brunner, Simon; Mora, André D; Fonseca, José M; Weber, Tina; Falkner-Radler, Christiane I; Oeser, Reinhard; Binder, Susanne. 2012. "Monitoring of Drusen and Geographic Atrophy Area Size after Cataract Surgery using the MD3RI Tool for Computer-Aided Contour Drawing", Ophtalmologica, 1: 1 - 10.
    doi: 10.1159/000345492
  • Correia, Raul C; Fonseca, J.M.; Donnellan, Andrew. 2012. "Ontology: A Support Structure for a V-Labs Network: Euronet-Lab", International Journal of Online Engineering (iJOE) 8, S3: 26 - 35.
    doi: 10.3991/ijoe.v8iS3.2257
    Mora, André D; Vieira, Pedro M; Manivannan, Ayyakkannu; Fonseca, José M. 2011. "Automated drusen detection in retinal images using analytical modelling algorithms", BioMedical Engineering OnLine 10, 1: 1 - 15.
    doi: 10.1186/1475-925X-10-59
  • Fernandes, Ana S; Fonseca, Jose M; Jarman, Ian H; Etchells, Terence A; Lisboa, Paulo J; Biganzoli, Elia; Bajdik, Chris. 2009. "Evaluation of missing data imputation in longitudinal cohort studies in breast cancer survival", International Journal of Knowledge Engineering and Soft Data Paradigms 1, 3: 257 - 276.
    doi: 10.1504/IJKESDP.2009.028818
  • Farinha, Ricardo J. P. C; Ruotsalainen, Ulla; Hirvonen, Jussi; Tuominen, Lauri; Hietala, Jarmo; Fonseca, José M; Tohka, Jussi. 2009. "Segmentation of Striatal Brain Structures from High Resolution PET Images", International Journal of Biomedical Imaging 2009, 1: 1 - 12.
    doi: 10.1155/2009/156234
  • Almeida, P. L; Kundu, S.; Beja, D.; Fonseca, J.; Figueirinhas, J. L; Godinho, M. H. 2009. "Deformation of isotropic and anisotropic liquid droplets dispersed in a cellulose liquid crystalline derivative", Cellulose 16, 3: 427 - 434.
    doi: 10.1007/s10570-008-9273-x
  • Bulajic, D; Cristoforetti, G; Corsi, M; Hidalgo, M; Legnaioli, S; Palleschi, V; Salvetti, A; Tognoni, E; Green, Steve; Bates, Derek; Steiger, Adolf; Fonseca, Josè; Martins, Josè; McKay, John; Tozer, Bryan; Wells, David; Wells, Robert; Harith, M.A. 2002. "Diagnostics of high-temperature steel pipes in industrial environment by laser-induced breakdown spectroscopy technique: the LIBSGRAIN project", Spectrochimica Acta Part B: Atomic Spectroscopy 57, 7: 1181 - 1192.
    doi: 10.1016/S0584-8547(02)00060-5
  • De Oliveira, E; Fonseca, Jose M; Steiger-Garcao, Adolfo. 1997. "Maciv a dai based resource management system", Applied Artificial Intelligence 11, 6: 525 - 550.
    doi: 10.1080/088395197118055

Trabalhos completos/resumidos em eventos com arbitragem científica
  • Cordeiro, Raúl; Donnellan, Andrew; Fonseca, José M. 2012. "Euronet Lab - A Cloud Based Laboratory Environment", Trabalho apresentado em IEEE EDUCON2012 - Collaborative Learning & New Pedagogic Approaches in Engineering Education, In Proceedings of IEEE EDUCON 2012, Marraquexe, 17-20 Abril.
  • Almeida, Graça; Melicio, Fernando; Fonseca, José M. 2012. "Block Matching Algorithms for Load tests Evaluation: ARPS versus PSO", Trabalho apresentado em The Eighth International Conference on Engineering Computational Technology, In Proceedings of The Eighth International Conference on Engineering Computational Technology, Dubrovnik, Croatia.
  • Silveira, Tiago; Kozakevicius, Alice; Fonseca, José M; Mora, André D. 2012. "Uma proposta de segmentacão de imagens de bactérias Eschirichia Coli obtidas por microscopia de fluorescência", Trabalho apresentado em 34º Congresso Nacional de Matemática Aplicada e Computacional, In Actas do 34º Congresso Nacional de Matemática Aplicada e Computacional, Águas de Lindôa.
  • Martins, Leonardo; Ribeiro, Andre S; Mäkelä, Jarno; Häkkinen, Antti; Fonseca, José M. 2012. "Stochastic model of transcription initiation of closely spaced promoters in Escherichia coli", Trabalho apresentado em Ninth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, In Proceedings of the Ninth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, Houston, Texas.
  • Queimadelas, Cátia; Rodrigues, João; Muthukrishnan, A-B.; Mora, André D; Ribeiro, Andre S; Fonseca, José M. 2012. "Segmentation and tracking of Escherichia coli expressing tsr-venus proteins from combined DIC/Fluorescence images", Trabalho apresentado em MEDSIP 2012 - 5th International Conference on Advances in Medical Signal and Information Processes , In Proceedings of MEDSIP 2012, Liverpool.
  • Fonseca, José M; Grieger, Björn; Mora, André D; Almeida, Miguel; Costa, Marco; Antunes, Luís; Fernandes, Vera. 2012. "SMARTIC - EXPLORING SMART-1 IMAGES", Trabalho apresentado em The Global Space Exploration Conference, In Proceedings of The Global Space Exploration Conference, Washington.
  • Fonseca, José M; Cordeiro, Raúl; Donnellan, Andrew. 2012. "Ontology: a support structure for a v-labs network, the Euronet-lab", Trabalho apresentado em REV2012 - Remote Engineering & Virtual Instrumentation, In Proceedings of REV 2012, Bilbao.
  • Rybanský, M.; Dorotovic, Ivan; Lorenc, M.; Shahamatnia, Ehsan; Ribeiro, Rita A; Fonseca, José M. 2012. "Search for jet stream", Trabalho apresentado em 21st National Solar Physics Meeting, In Proceedings of the 21st National Solar Physics Meeting, Stará Turá.
  • Fonseca, José M; Grieger, Björn; Mora, André D; Almeida, Miguel; Costa, Marco; Antunes, Luís; Fernandes, Vera. 2012. "Calibration and Mosaicing of SMART-1 Images", Trabalho apresentado em European Planetary Science Congress, In Proceedings of the European Planetary Science Congress 2012, Madrid.
  • Fonseca, Jose M; Rodrigues, Nuno M; Mora, Andre D; Ribeiro, Rita A. 2011. "Optical character recognition using automatically generated Fuzzy classifiers", Trabalho apresentado em 2011 Eighth International Conference on Fuzzy Systems and Knowledge Discovery (FSKD), In 2011 Eighth International Conference on Fuzzy Systems and Knowledge Discovery (FSKD), Shanghai, China.
    doi: 10.1109/FSKD.2011.6019585
  • Shahamatnia, Ehsan; Dorotovic, Ivan; Ribeiro, Rita A; Fonseca, José M. 2011. "Swarm Intelligence and Snake Model For Automatic Sunspot Tracking ", Trabalho apresentado em AI in Space: Intelligence beyond planet Earth, In Proceedings of the AI in Space: Intelligence beyond planet Earth Workshop, Barcelona.
  • Almeida, Graça; Fonseca, José M; Melicio, Fernando. 2011. "Displacement measurements with block motion algorithms", Trabalho apresentado em VIPIMAGE - III ECCOMAS Thematic Conference on Computational Vision and Medical Image Processing, In Proceedings of the III ECCOMAS Thematic Conference on Computational Vision and Medical Image Processing: VipIMAGE 2011, Olhão.
  • Lisboa, Paulo J. G; Fernandes, Ana S; Fonseca, Jose M; Bajdik, Chris; Biganzoli, Elia. 2010. "Assessment of benefit vs. risk of drug therapy: The potential for outcome analysis with flexible models", Trabalho apresentado em 2010 International Joint Conference on Neural Networks (IJCNN), In The 2010 International Joint Conference on Neural Networks (IJCNN), Barcelona, Spain.
    doi: 10.1109/IJCNN.2010.5596689
  • Fernandes, Ana S; Bacciu, Davide; Jarman, Ian H; Etchells, Terence A; Fonseca, José M; Lisboa, Paulo J. G. 2009. "p-Health in Breast Oncology: A Framework for Predictive and Participatory e-Systems", Trabalho apresentado em 2009 Second International Conference on Developments in eSystems Engineering (DESE), In 2009 Second International Conference on Developments in eSystems Engineering, Abu Dhabi, UAE.
    doi: 10.1109/DeSE.2009.68
  • Alves, David S; Paulus, Jouni; Fonseca, José M. 2009. "Drum Transcription from Multichannel Recordings with Non-Negative Matrix Factorization", Trabalho apresentado em 17th European Signal Processing Conference (EUSIPCO 2009), In Proceedings of the 17th European Signal Processing Conference, Glasgow, Scotland.
  • Fernandes, Ana S; Jarman, Ian H; Etchells, Terence A; Fonseca, José M; Biganzoli, Elia; Bajdik, Chris; Lisboa, Paulo J. G. 2008. "Missing Data Imputation in Longitudinal Cohort Studies: Application of PLANN-ARD in Breast Cancer Survival", Trabalho apresentado em 2008 Seventh International Conference on Machine Learning and Applications, In 2008 Seventh International Conference on Machine Learning and Applications, San Diego, CA, USA.
    doi: 10.1109/ICMLA.2008.106
  • Fonseca, José M; Mora, André D; Vieira, Pedro. 2005. "Detecção de Drusas em Imagens de Retinografia", Trabalho apresentado em Jornadas de Engenharia Electrónica e Telecomunicações e de Computadores - JETC'05. ISEL, Lisboa, Portugal - 17-18 November 2005, In Jornadas de Engenharia Electrónica e Telecomunicações e de Computadores - JETC'05, Lisboa.
  • Fonseca, José M; Mora, André D; Marques, Ana C. 2005. "MAMIS - Um Sistema Multi-agente para Informação Médica", Trabalho apresentado em Jornadas de Engenharia Electrónica e Telecomunicações e de Computadores - JETC'05. ISEL, Lisboa, Portugal - 17-18 November 2005, In Jornadas de Engenharia Electrónica e Telecomunicações e de Computadores - JETC'05, Lisboa.
  • Iglesias, O.; Ribeiro, R.A.; Fonseca, J.R.. 2004. "A fuzzy multi-agent bidding model", Trabalho apresentado em Proceedings. IEEE/WIC/ACM International Conference on Intelligent Agent Technology, 2004. (IAT 2004)., In Proceedings. IEEE/WIC/ACM International Conference on Intelligent Agent Technology, 2004. (IAT 2004)., Beijing, China.
    doi: 10.1109/IAT.2004.1343009
  • Mora, A.; Fonseca, J.; Martins, J.; Steiger-Garcao, A.. 2003. "LIBS chemical images analysis for fatigue estimation in industrial materials", Trabalho apresentado em 3rd International Symposium on Image and Signal Processing and Analysis, 2003. ISPA 2003., In 3rd International Symposium on Image and Signal Processing and Analysis, 2003. ISPA 2003. Proceedings of the, Rome, Italy.
    doi: 10.1109/ISPA.2003.1296920
  • De Oliveira, E; Fonseca, José M; Jennings, Nick. 1999. "Learning to be Competitive in the Market", Trabalho apresentado em AAAI Workshop on Negotiation: Settling Conflicts and Identifying Opportunities, In AAAI Technical Report WS-99-12. Compilation, Orlando.
  • De Oliveira, E; Fonseca, José M; Steiger-Garcao, Adolfo. 1999. "Multi-Criteria Negotiation on Multi-Agent Systems", Trabalho apresentado em CEEMAS'99 - First International Workshop of Central and Eastern Europe on Multi-Agent Systems, 30 May-3 June 1999, In Proceedings of CEEMAS'99 , S. Petersburgo, Rússia.
    Ribeiro-Fonseca, J.; Correia, L.. 1994. "Identification of underwater acoustic noise", Trabalho apresentado em OCEANS'94, In Proceedings of OCEANS'94, Brest, France.
    doi: 10.1109/OCEANS.1994.364112
  • Fonseca, J.M.; Moura-Pires, F.. 1992. "Ship Noise Evaluation Based On Segmented Decision Trees", Trabalho apresentado em IEEE/RSJ International Conference on Intelligent Robots and Systems, In Proceedings of the IEEE/RSJ International Conference on Intelligent Robots and Systems, Raleigh, NC.
    doi: 10.1109/IROS.1992.601419
  • Fonseca, José M; Barata, Manuel M; Steiger-Garção, Adolfo. 1990. "Predictive Monitoring Environment for CNC Machining", Trabalho apresentado em IEEE International Workshop on Intelligent Motion Control, Istambul, Turquia, Agosto 1990, In Proccedings, Istambul.


Trabalhos completos/resumidos em eventos sem arbitragem científica
  • Almeida, Miguel; Fonseca, José M. 2011. "Pattern recognition for the creation of synthetic flat fields", Trabalho apresentado em Inter-Departmental Science Workshop 2011 - IDSW 2011, In Proceedings of the Inter-Departmental Science Workshop 2011 , Toledo.
  • Patentes Nacionais
  • Fonseca, José M. ARINCA - Armazém Seguro de Cartões de Identificação Personalizados,2008. Natureza do produto: Equipamento. Patente: Modelo Industrial/Modelo.n. 104061,"Armazém Seguro de Cartões de Identificação Personalizados".26 set. 2011(Depósito);10 jul. 2008(Concessão).


Apresentação oral de trabalho
  • Fonseca, José M; Mora, André D. Biomedical Applications of Digital Image Processing,JORTEC2013 - Biomedical Engineering, A Glance at the Future,Lisboa,2013 (Conferência ou palestra).
  • Brunner, Simon; Mora, André D; Fonseca, José M; Weber, Tina; Falkner-Radler, Christiane I; Oeser, Reinhard; Binder, Susanne. Drusen and geographic atrophy quantification with the MD3RI Tool in non-exsudative AMD before and after cataract surgery: a short-term prospective randomized trial,2nd Workshop on Data Analysis and Modeling Retina in Health and Disease ,Costa da Caparica,2012 (Comunicação).
  • Cordeiro, Hugo; Menezes, Carlos; Fonseca, José M. Voice Pathology Detection and identification using speech processing techniques,3rd Doctoral Conference on Computing, Electrical and Industrial Systems (DoCEIS'12),Costa da Caparica,2012 (Poster).
  • Dorotovic, Ivan; Shahamatnia, Ehsan; Lorenc, Marc; Rybanský, Marc; Ribeiro, Rita A; Fonseca, José M. Differential Rotation of Coronal Bright Points Determined using PSO/Snake Algorithms,European Week of Astronomy and Space Science 2012,Roma,2012 (Poster).
  • Fonseca, José M; Cordeiro, Raúl; Donnellan, Andrew. Euronet Lab, a Cloud V-Lab Environment,DOCEIS 2011, 2nd Doctoral Conference on Computing, Electrical and Industrial Systems,Costa da Caparica,2011 (Poster).
  • Fonseca, José M; Gomes, Carla; Costa, Ruy. Artificial Intelligence for b-learning effectiveness evaluation,DOCEIS 2011, 2nd Doctoral Conference on Computing, Electrical and Industrial Systems,2011 (Poster).
  • Assadi, Amir; Ribeiro, Rita A; Fonseca, José M; Mora, André D; Campanella, Gianluca. Model Reduction of Massive High Dimensional Biological Image Data and Soft Computing,World Conference on Soft Computing, San Francisco State University, San
  • Francisco, USA, May 23-26,San Francisco,2011 (Comunicação).
  • Fonseca, José M. Photogrammetric and Civil Engineering,DOCEIS 2010, Doctoral Conference on Computing, Electrical and Industrial Systems, 22-24 February 2010, Costa da Caparica, Portugal,Costa da Caparica,2010 (Poster).
  • Fonseca, José M; Meira, Manuel; Mora, André D; Elias, Jorge. SINAIS - AIS based navigational-aid system,28th Waterborne Transport Committee Meeting,Venice ,2009 (Comunicação).
  • Dorotovic, Ivan; Fernandes, João; Fonseca, José M; Moreira, Carlos; Ribeiro, Rita A. COSIS: Coimbra Observatory Solar Information System,2006 (Poster).
  • Fonseca, José M; De Oliveira, E; Steiger-Garção, Adolfo. Negotiation and Resources Cost Calculation in a MAS for Civil Construction Companies,MAMAAW'97; Ronneby, Sweden, June 1997,Ronneby, Sweden,1997 (Poster).



Researcher at CRI/UNINOVA
Professor at DEE-FCT/UNL
jmf@uninova.pt Edifício Researcher at CTS / UNINOVA, Gab. 2.15
+351 21 294 85 27/8/9 (ext. 13734)