Publications
Proceedings – Book Chapters – Journals
– Conferences - Patents
Edited Books and Proceedings
2. D. Mery
and L. Rueda. Advances in Image
and Video Technology, Proceedings of the IEEE
Pacific-Rim Symposium on Image and Video Technology (PSIVT 2007). Lecture
Notes in Computer Science (LNCS), Vol. 4872, Springer, 2007. 1. L. Rueda, D. Mery and J. Kittler.
Progress in Pattern Recognition, Image Analysis and Applications, Proceedings
of the 12th Iberoamerican Congress on
Pattern Recognition (CIARP 2007), Lecture Notes in Computer Science
(LNCS), Vol. 4756, Springer, 2007. Book Chapters
4. D. Rojas, L. Rueda, H. Urrutia, A. Ngom, and G.
Carcamo, Automatic Segmentation Methods and Applications to Biofilm Image
Analysis, Data Mining in Biomedical Signaling, Imaging and Systems, CRC
Press, 2011. 3. N. Subhani, L. Rueda, A. Ngom, On Clustering Gene
Expression Time-series Signals, Data Mining in Biomedical Signaling, Imaging
and Systems, CRC Press, 2011. 2. B. John Oommen and L. Rueda, Stochastic
Learning-based Weak Estimation of Multinomials and
Its Applications to Pattern Recognition and Data Compression,
Knowledge-Based Intelligent System Advancements: Systemic and Cybernetic
Approaches, IGI Global Publishers, ISBN 978-1-61692-811-7, 2010, pp. 1-29. 1. L. Rueda and A. Bari, Clustering
Time-series Gene Expression Data, Oligonucleotide Array Sequence
Analysis, Nova Science Publishers, ISBN 978-1-60456-542-3, 2008, pp. 121-159. Journals
29. Md. Aziz, M. Maleki, L.
Rueda, M. Raza, S. Banerjee, Prediction
of Biological Protein-protein Interactions using Atom-type and Amino Acid
Properties, Proteomics, 2011, pp. 3802–3810, DOI: 10.1002/pmic.201100186. 28. L. Rueda, I. Rezaeian, A
Fully Automatic Gridding Method for cDNA Microarray
Images, BMC Bioinformatics, 2011, 12:113. 27. D. Rojas, L. Rueda, H. Urrutia, A. Ngom, G. Carcamo, Image Segmentation of
Biofilm Structures Using Optimal Multi-Level Thresholding,
International Journal of Data Mining and Bioinformatics, 2011, 5(3):266-286. 26. A. Ngom, L. Rueda,
L. Wang, R. Gras, Selection
Based Heuristics for the Non-Unique Oligonucleotide Probe Selection Problem
in Microarray Design, Pattern
Recognition Letters, 31(14): 2113-2125 (2010).. 25. N. Subhani, L. Rueda,
A. Ngom, C. Burden, “Multiple
Gene Expression Profile Alignment for Microarray Time-series Data Clustering”,
Bioinformatics, 2010,
26(18):2281-2288. 24. L. Rueda, B. J.
Oommen, C. Henriquez, Multi-class Pairwise
Linear Dimensionality Reduction Using Heteroscedastic
Schemes, Pattern Recognition, 43
(2010), pp. 2456-2465. 23. P. Jopia, N. Ruiz-Tagle, M. Villagrán,
K. Sossa, S. Pantoja, L. Rueda, H. Urrutia, Biofilm
Growth Kinetics of a Monomethylamine Producing Alphaproteobacteria Strain Isolated from an Anaerobic
Reactor. Anaerobe, 16(2010),
pp. 19-26. 22. L. Rueda and M. Herrera, A Theoretical
Comparison of Two-class Fisher's and Heteroscedastic
Linear Dimensionality Reduction Schemes, Pattern Recognition Letters,
Vol. 29, 2008, pp. 2092-2098. 21. L. Wang, A. Ngom, L. Rueda, R. Gras, Selection
Based Heuristics for the Non-Unique Oligonucleotide Probe Selection Problem,
Springer Trans. on Computational
Systems Biology, Springer, LNBI
5410, 2008, pp. 143-162. 20. L. Rueda, A. Bari, A. Ngom, Clustering
Time-series Gene Expression Data with Unequal Time Intervals, Springer Trans. on Computational Systems
Biology, Springer, LNBI 5410,
2008, pp. 100-123. 19. L. Rueda and B. John Oommen, An
Efficient Compression Scheme for Data Communication which Uses a New Family
of Self-Organizing Binary Search Trees, International Journal of Communication Systems, Vol. 21, 2008, pp. 1091-1120. 18. L. Rueda and M. Herrera, Linear Dimensionality
Reduction by Maximizing the Chernoff Distance in
the Transformed Space, Pattern
Recognition, Vol. 41, Issue 10, 2008, pp. 3138-3152. 17. W. Yang, L. Rueda
and A. Ngom, On
Finding the Best Parameters of Fuzzy k-Means
for Clustering Microarray Data, Multiple-Valued
Logic and Soft-Computing Journal, 2007, Vol. 13, 2007, pp. 145-178. 16. B. Schell, M. Vargas Martin, P. Hung, and L. Rueda, Cyber Child Pornography: A
Review Paper of the Social and Legal Issues and Remedies—and A Proposed
Technological Solution, Aggression
and Violent Behavior, Vol. 12, 2007, pp. 45-63. 11. B. J. Oommen and L. Rueda, Stochastic
Learning-based Weak Estimation of Multinomial Random Variables and Its
Applications to Pattern Recognition in Non-stationary Environment, Pattern Recognition, Vol. 39, 2006,
pp. 328-341. 7. B. J. Oommen and L.
Rueda, A Formal
Analysis of Why Heuristics Work. Artificial Intelligence, Vol.
164, 2005, pp. 1-22.
2. B. J. Oommen and L.
Rueda, The
Efficiency of Modern-Day Histogram-Like Techniques for Query Optimization.
The Computer Journal, Vol. 45, No.
5, 2002, pp. 494-510.
Conferences
67. A. Jafarian, A. Ngom,
L. Rueda, A Novel Recursive
Feature Subset Selection Algorithm, 11th
IEEE International Conference on Bioinformatics and Bioengineering
(BIBE 2011), Taichung, Taiwan, 2011, DOI
10.1109/BIBE.2011.19. 66. A. Jafarian, A. Ngom,
L. Rueda, New Gene Subset
Selection Approaches Based on Linear Separating Genes and Gene-Pairs, 6th
IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB
2011), Delft, The Netherlands, 2011, pp. 50-62. 65. L. Rueda, I. Rezaeian, Applications of Multilevel Thresholding Algorithms to Transcriptomics
Data, 16th Iberoamerican Congress on Pattern Recognition, Pucón,
Chile, 2011, LNCS 7042, PP. 26-37. Plenary talk. 64. L. Rueda, I. Rezaeian, Automatic Algorithms for Analysis of cDNA Microarray and Chip-seq
Data, Microarray World Congress, San Francisco, USA, 2011. Invited talk. 63. M. Maleki, Md. Aziz, L. Rueda, Analysis of Obligate and
Non-obligate Complexes using Desolvation Energies
in Domain-domain Interactions, 10th International Workshop on Data Mining in
Bioinformatics (BIOKDD 2011) in conjunction with ACM SIGKDD 2011, San Diego,
USA, 2011, pp. 21-26. 62. I. Rezaeian, L. Rueda, Biological Assessment of
Grid and Spot Detection in cDNA Microarray Images,
ACM Conference on Bioinformatics, Computational Biology and Biomedicine,
Chicago, USA, 2011. To be presented. 61. Y. Li, A. Ngom, L. Rueda, A Framework of Gene Subset
Selection Using Multiobjective Evolutionary
Algorithm, 2011 IEEE Congress on Evolutionary Computation, New Orleans, USA,
2011. 60. M. Maleki, Md. Aziz,
L. Rueda, M. Raza, S. Banerjee, “Domain-domain
Interactions in Transient and Obligate Protein-protein Complexes”, Systems
Biology Symposium, Ann Arbor, MI, USA, 2011. Poster presentation. 59. I. Rezaeian, L. Rueda, A Parameterless Automatic Spot Detection Method for cDNA Microarray Images, 3rd IEEE International
Conference on Bioinformatics & Biomedicine, Hong Kong, 2010, pp. 388-392.
58. L. Rueda, S. Banerjee, Md. Aziz, M. Raza, Protein-protein
Interaction Prediction using Desolvation Energies
and Interface Properties, 3rd IEEE International Conference on
Bioinformatics & Biomedicine, Hong Kong, 2010, pp. 17-22. 57. I. Rezaeian, L. Rueda, Sub-grid and
Spot Detection in DNA Microarray Images using Optimal Multi-level Thresholding, 5th IAPR International Conference on
Pattern Recognition in Bioinformatics (PRIB 2010), Nijmegen, The Netherlands,
2010, pp. 277-288. 56. L.
Rueda, C. Garate, S. Banerjee, Md. Mominul Aziz, Biological
Protein-protein Interaction Prediction using Binding Free Energies and Linear
Dimensionality Reduction, 5th IAPR International Conference on Pattern
Recognition in Bioinformatics (PRIB 2010), Nijmegen, The Netherlands, 2010,
pp. 383-394. 55. Y. Li, N. Subhani, A.
Ngom, L. Rueda, Alignment-based
versus Variation-based Transformation Methods for Clustering Microarray
Time-Series Data, 2010 ACM International Conference on Bioinformatics and
Computational Biology (ACM-BCB 2010), Niagara Falls, USA, 2010, pp.
53-61. 54. N. Subhani, Y. Li, A.
Ngom, L. Rueda, Alignment
versus Variation Methods for Clustering Microarray Time-Series Data, 2010
IEEE World Congress on Computational Intelligence (WCCI 2010), Barcelona,
Spain, 2010, pp. 818-825. 53. Y. Li, A. Ngom, L. Rueda, Missing
Value Imputation Methods for Gene-Sample-Time Microarray Data Analysis,
2010 IEEE Symposium on Computational Intelligence in Bioinformatics and
Computational Biology (CIBCB 2010), Montreal, Canada, 2010, pp. 183-189. 52. N. Subhani, L. Rueda,
A. Ngom, C. Burden, New
Approaches to Clustering Microarray Time-Series Data Using Multiple
Expression Profile Alignment, 2010 IEEE Symposium on Computational
Intelligence in Bioinformatics and Computational Biology (CIBCB 2010),
Montreal, Canada, 2010, pp. 170-176. 51. N. Subhani, A. Ngom, L. Rueda, C. Burden, Clustering
Microarray Time-series Data using Expectation Maximization and Multiple
Profile Alignment, Applications of Machine Learning in Bioinformatics
Workshop (held at BIBM 2009), Washington, D.C., USA, 2009, pp. 2-7. 50. D. Rojas, L. Rueda, A. Ngom, H. Urrutia, G. Carcamo, Biofilm Image
Segmentation Using Optimal Multi-Level Thresholding,
IEEE International Conference on Bioinformatics & Biomedicine (BIBM
2009), Washington, D.C., USA, 2009, pp. 185-190. 49. L. Rueda, J. Rojas, A Pattern
Classification Approach to DNA Microarray Image Segmentation, 4th IAPR International Conference on
Pattern Recognition in Bioinformatics (PRIB 2009), Sheffield, UK,
Springer, 2009, LNCS 5780, pp. 319-330. 48. D. Rojas, L. Rueda, H. Urrutia, A. Ngom, Efficient Optimal
Multi-Level Thresholding for Biofilm Image
Segmentation, 4th IAPR
International Conference on Pattern Recognition in Bioinformatics (PRIB 2009),
Sheffield, UK, 2009, LNCS 5780, 2009, pp. 307-318. 47. N. Subhani, A. Ngom, L. Rueda, C. Burden, Microarray
Time-Series Data Clustering via Multiple Alignment of Gene Expression
Profiles, 4th IAPR International
Conference on Pattern Recognition in Bioinformatics (PRIB 2009),
Sheffield, UK, 2009, LNCS 5780, 2009, pp. 377-390. 46. M. Pinninghoff, R. Contreras, L. Rueda, An Evolutionary
Approach for Correcting Random Amplified Polymorphism DNA Images, 3rd International Work Conference on the
Interplay between Natural and Artificial Computation (IWINAC 2009),
Santiago de Compostela, Spain, LNCS 5602, 2009, pp.
469-477. 45. V.A. Gallardo, H. Urrutia, N. Ruiz-Tagle, C. Espinoza, L. Rueda, A. Ngom, C. Monsalve, A.
Fonseca, J. Gutierrez, S. Rojas and L. Abarzua, High Throughput Sequencing to
Assess Benthic Bacteria Biodiversity off Central Chile, Census of Marine Life
Synthesis Workshop, (CoML 2009), February 1-5, Long
Beach, California, 2009. 44. L. Rueda, An
Efficient Algorithm for Optimal Multilevel Thresholding
of Irregularly Sampled Histograms, 7th
International Workshop on Statistical Pattern Recognition (S+SSPR 2008),
Orlando, Florida, USA, Springer, LNCS 5432, 2008, pp. 612-621. 43. A. Bari, L. Rueda,
A. Ngom, “Microarray Time-Series Data
Classification via Multiple Alignment of Gene Expression Profiles”, Third
IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB
2008), Melbourne, Australia, Supplementary Proceedings, ISBN
978-0-7326-2226-8, 2008, pp. 25-36. 42 X. Li, A. Ngom and L. Rueda, Minimal siRNA
Set Cover Heuristic for Gene Family Knockdown, Third IAPR International
Conference on Pattern Recognition in Bioinformatics (PRIB 2008), Melbourne,
Australia, Supplementary Proceedings, ISBN 978-0-7326-2226-8, 2008, pp.
37-48. 41. L. Wang, A. Ngom, L. Rueda, Sequential Forward
Selection Approach to the Non-Unique Oligonucleotide Probe Selection Problem,
Third IAPR International Conference on
Pattern Recognition in Bioinformatics (PRIB 2008), Melbourne, Australia,
2008, Springer, LNBI 5265, pp. 262-275. 40. L. Rueda, C. Henriquez, B. J. Oommen, Chernoff-Based
Multi-class Pairwise Linear Dimensionality Reduction, Proceedings of the 13th Iberoamerican Congress on Pattern
Recognition (CIARP 2007), Havana, Cuba, 2008, LNCS 5197, pp. 301-308. 39. L. Wang, A. Ngom, R.
Gras, L. Rueda, Evolution Strategy with
Greedy Probe Selection Heuristics for the Non-Unique Oligonucleotide Probe
Selection Problem, 5th Conference
on Computational Intelligence in Bioinformatics and Bioengineering (CIBCB
2008), Sun Valley, Idaho, USA, 2008, pp. 54-61. Recognized for the Overall Best Paper Award. 38. V. Gallardo, A. Teske, J. L. Nielsen, H. Urrutia, N. Ruiz-Tagle, C.
Espinoza, L. Abarzua, D. Andrades, L.
Rueda, C. Monsalve, 16S Ribosomal RNA Gene Sequence Analysis of Sediment Macrobacteria from the Central Chile Oxygen Minimum Zone,
12th Biennial Symposium on Microbial
Ecology (ISME-12), Cairns, Australia, 2008. Poster presentation. 37. L. Rueda, Sub-grid Detection in
DNA Microarray Images, Proceedings of
the IEEE Pacific-RIM Symposium on Image and Video Technology, Santiago,
Chile, 2007, LNCS 4872, pp. 248-259. 36. L. Rueda and A. Bari, Clustering Temporal Gene Expression Data
with Unequal Time Intervals, Proceedings of the 2nd International Conference on Bio-Inspired Models of Network,
Information, and Computing Systems (BIONETICS 2007), Bioinformatics
Track. 35. L. Rueda and B.J. Oommen, A New Approach to Adaptive Encoding
Data using Self-organizing Data Structures, Proceedings of the 22nd International Symposium on
Computer and Information Sciences, Ankara, Turkey, 2007, pp.15-20. 34. L. Rueda, O. Uyarte, S. Valenzuela and J. Rodriguez, Processing Random
Amplified Polymorphysm DNA Images Using the Radon
Transform and Mathematical Morphology, Proc. of the 4th International Conference on Image Analysis and
Recognition, Montreal, Canada, 2007, LNCS 4633, pp. 1071-1081. 33. T. Gutierrez, L. Rueda, J. Martinez, M. Bunster,
“Finding Discriminant Features in Interaction Sites for Identifying Transient
and Obligate Protein-protein Complexes”, Bioinformatics 2007, Joint
Collaborative Workshop of the European Molecular Biology Network (EMBnet) and the Iberoamerican Bioinformatics Network
(RIBIO), Malaga, Spain, 2007. Poster presentation. 32. L. Rueda and M.
Herrera, A New Approach to
Multi-class Linear Dimensionality Reduction, Proc. of the 11th Iberoamerican Congress on Pattern Recognition,
Cancun, Mexico, 2006, LNCS 4225, pp. 634-643. 31. L. Rueda and M.
Herrera, A Theoretical
Comparison of Two Linear Dimensionality Reduction Techniques, Proc. of the 11th Iberoamerican Congress
on Pattern Recognition, Cancun, Mexico, 2006, LNCS 4225, pp. 624-633. 30. L. Rueda and M.
Herrera, A New Linear
Dimensionality Reduction Technique based on Chernoff
Distance, Proc. of the 10th
Ibero-American Conference on Artificial
Intelligence, Ribeirao Preto, Brazil, 2006,
LNAI 4140, pp. 299-308. 29. M. Ali, L. Rueda,
and M. Herrera, On the Performance of Chernoff-distance-based Linear Dimensionality Reduction
Techniques, Proc. of the 19th Canadian Conference on
Artificial Intelligence, Quebec, Canada, 2006, Springer, LNAI 4013, pp.
469-480. 28. A. Bari and L.
Rueda, A New Profile Alignment Method
for Clustering Gene Expression Data, Proc. of the 19th Canadian Conference on
Artificial Intelligence, Quebec, Canada, 2006, Springer, LNAI 4013, pp.
86-97. 27. M. Chopra, M. Vargas Martin, L. Rueda, P.C.K. Hung.
Toward New Paradigms to
Combating Internet Child Pornography. Proc. of the IEEE
Canadian Conference on Electrical and Computing Engineering (CCECE '06), 26. M. Chopra, M. Vargas-Martin, L. Rueda and P. Hung,
A Source
Address Reputation System to Combating Child Pornography at the Network Level, Proc. of the IADIS International
Conference on Applied Computing, San Sebastian, Spain, 2006, pp. 472-477. 25. L. Rueda and Y. Zhang, A Geometric Framework to
Visualize Fuzzy-clustered Data, Proc. of the XXV International Conference
of the Chilean Computer Science Society, Valdivia, Chile, 2005, pp. 13-20. 24. W. Yang, L. Rueda, and A. Ngom, A Simulated Annealing
Approach to Find the Optimal Parameters for Fuzzy Clustering Microarray Data,
Proc. the XXV International Conference of the Chilean Computer Science
Society, Valdivia, Chile, 2005, pp. 45-54. 23. L. Rueda and B. J.
Oommen, Efficient Adaptive
Data Compression using Fano Binary Search Trees.
Proc. of the 20th International Symposium on Computer and Information
Sciences, 22. B. J. Oommen and L. Rueda, On Utilizing Stochastic Learning
Weak Estimators for Training and Classification of Patterns with
Non-Stationary Distributions. Proc. of the 28th German Conference on
Artificial Intelligence (KI 2005), 21. L. Rueda and L. Qin, A New Method for DNA Microarray
Image Segmentation. Proc. of the International Conference on Image
Analysis and Recognition, 20. L. Rueda and V. Vidyadharan, A New Approach to Automatically
Detecting Grids in DNA Microarray Images. Proc. of the International
Conference on Image Analysis and Recognition, 19. L. French, A. Ngom and L. Rueda, Fast Protein Superfamily
Classification using Principal Component Null Space Analysis. Proc.
of the 18th Canadian Conference on 18. L. Rueda and L. Qin, An
Unsupervised Learning Scheme for DNA Microarray Image Spot Detection. Proc.
of the First International Conference on Complex Medical Engineering, 17. L. Rueda and Y. Zhang, A
New Approach for Visualizing Fuzzy-clustered Microarray Data. Proc. of
the 6th International Conference on Mathematics and Computers in Biology and
Chemistry, 16. L.
Rueda and V. Vidyadharan, A New Approach to
Automatically Detecting Grids in DNA Microarray Images, International Conference on Bioinformatics and its Applications
(ICBA’04), Fort Laurerdale, Florida, 2004.
Poster presentation. 12. B. J. Oommen and L. Rueda, A
New Family of Weak Estimators for Training in Non-Stationary Distributions,
Proc. of the Joint IAPR International Workshop on Statistical Pattern
Recognition,
7. B. J. Oommen and L.
Rueda, Using Pattern Recognition Techniques to Derive a Formal
Analysis of Why Heuristic Functions Work, Proc. of the 2nd International
Workshop on Pattern Recognition in Information Systems, Alicante, Spain,
April 2002, pp. 45-58.
3. B.J. Oommen and L.
Rueda, Histogram Methods in Query Optimization :
The Relation between Accuracy and Optimality, 7th International
Conference on Database Systems for Advanced Applications, 2. B.J. Oommen and L.
Rueda, An Empirical Comparison of Histogram-like Techniques for Query
Optimization, Proc of the 2nd International Conference on Enterprise
Information Systems (ICEIS), Stafford, UK, 2000, pp. 71-78.
Patents
1. Encryption
Possessing Statistical Perfect Secrecy and Stealth, B.J. Oommen and L.
Rueda. Click here for
an overview. |