Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
10th European Conference, EvoBIO 2012, Málaga, Spain, April 11-13, 2012, Proceedings
Published on 23. March 2012
XIII, 255 pages
978-3-642-29066-4 (ISBN)
Description
This book constitutes the refereed proceedings of the 10th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, EvoBIO 2012, held in Málaga, Spain, in April 2012 co-located with the Evo* 2012 events.
The 15 revised full papers presented together with 8 poster papers were carefully reviewed and selected from numerous submissions. Computational Biology is a wide and varied discipline, incorporating aspects of statistical analysis, data structure and algorithm design, machine learning, and mathematical modeling toward the processing and improved understanding of biological data. Experimentalists now routinely generate new information on such a massive scale that the techniques of computer science are needed to establish any meaningful result. As a consequence, biologists now face the challenges of algorithmic complexity and tractability, and combinatorial explosion when conducting even basic analyses.
The 15 revised full papers presented together with 8 poster papers were carefully reviewed and selected from numerous submissions. Computational Biology is a wide and varied discipline, incorporating aspects of statistical analysis, data structure and algorithm design, machine learning, and mathematical modeling toward the processing and improved understanding of biological data. Experimentalists now routinely generate new information on such a massive scale that the techniques of computer science are needed to establish any meaningful result. As a consequence, biologists now face the challenges of algorithmic complexity and tractability, and combinatorial explosion when conducting even basic analyses.
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Mario Giacobini | Leonardo Vanneschi | William S. Bush
Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
10th European Conference, EvoBIO 2012, Málaga, Spain, April 11-13, 2012, Proceedings
Book
03/2012
1st Edition
Springer
€53.49
Shipment within 7-9 days
Content
- Title page
- Preface
- Organization
- Table of Contents
- Oral Contributions
- Automatic Task Decomposition for the NeuroEvolution of Augmenting Topologies (NEAT) Algorithm
- Introduction
- NeuroEvolution of Augmenting Topologies
- The Modular Feed Forward ANN Architecture
- Approach
- Implementation
- Experiments
- Monks Third Problems
- Heart Disease Diagnosis
- Mass Spectral Peptide Data
- Discussion
- Promotion of the Dissemination of Useful Functionality
- Maximization of Useful Information Generated in Evaluations
- Reduction in the Complexity of Functions Evolved
- Conclusions and Future Work
- References
- Evolutionary Reaction Systems
- Introduction
- Preliminary Notions
- Evolutionary Reaction Systems
- Experimental Study
- Conclusions
- References
- Optimizing the Edge Weights in Optimal Assignment Methods for Virtual Screening with Particle Swarm Optimization
- Introduction
- Methods
- Optimal Assignment Kernel
- Edge Weight Optimization
- Experimental Setup
- Results
- Discussion and Conclusion
- References
- L´evy-Flight Genetic Programming: Towards a New Mutation Paradigm
- Introduction
- Background
- Lévy Walks and Flights as Optimal Search Strategies
- Genetic Programming and Linear Genetic Programming
- LGP with Lévy-Flight Mutation
- Experimental Results
- Boolean Regression
- Numeric Regression: The Mexican Hat Function
- Numeric Regression: Quartic Polynomial Regression
- Discussion, Conclusions, and Future Work
- References
- Understanding Zooplankton Long Term Variability through Genetic Programming
- Introduction
- Data and Methods
- Data
- Genetic Programming
- Training and Validation and Genotype Analysis
- Relevant Environmental Variables and Zooplankton Abundance Prediction
- Conclusion and Future Work
- References
- Inferring Disease-Related Metabolite Dependencies with a Bayesian Optimization Algorithm
- Introduction
- Background
- State of the Art
- Methods
- The Bayesian Optimization Algorithm
- Experimental Design
- Results and Discussion
- Classification Accuracy
- Reproducibility of Edges
- Networks of Dependent Metabolites
- Physiological Interpretation
- Conclusions
- References
- A GPU-Based Multi-swarm PSO Method for Parameter Estimation in Stochastic Biological Systems Exploiting Discrete-Time Target Series
- Introduction
- Parameter Estimation of Stochastic Biological Systems
- Formalization of the Problem
- Fitness Function
- Multi-swarm PSO
- Implementation and Discussion of the Methodology
- A GPU-Based Multi-swarm PSO
- Results
- Conclusions
- References
- Tracking the Evolution of Cooperation in Complex Networked Populations
- Introduction
- Results and Discussion
- Evolution of Cooperation in Finite Well-Mixed Populations
- Gradients of Selection in Structured Populations
- Results for Homogeneous Networks
- Results for Heterogeneous Networks
- Conclusions
- References
- GeNet: A Graph-Based Genetic Programming Framework for the Reverse Engineering of Gene Regulatory Networks
- Introduction
- GeNet
- Case Studies
- Results
- Conclusions and Future Work
- References
- Comparing Multiobjective Artificial Bee Colony Adaptations for Discovering DNA Motifs
- Introduction
- Motif Discovery Problem: Review and Formulation
- Brief Review of MDP Related Works
- Multiobjective Formulation of MDP
- MDP Example
- Artificial Bee Colony
- Original ABC Algorithm
- Multiobjetive ABC Algorithm
- Experimental Results
- Conclusions and Future Work
- References
- The Role of Mutations in Whole Genome Duplication
- Introduction
- Background
- Methods
- RBN Topology
- Genome Wide Duplication and Duplication Mutation
- Environmental Robustness
- Evolutionary Innovation
- Evolution and Evolutionary Mutation
- Experimental Results
- Duplication Mutations in an Ancestral Environment
- Effects of Mutations on Evolutionary Innovation
- Survival of the Duplicated RBNs
- Discussion
- References
- Comparison of Methods for Meta-dimensional Data Analysis Using in Silico and Biological Data Sets
- Introduction
- A Systems Biology Approach for Complex Genetic Traits
- Methods
- Data Simulation
- Data Analysis
- Results
- Random Jungle and Lasso
- ATHENA
- Combination Approach on Biological Data
- Discussion
- References
- Inferring Phylogenetic Trees Using a Multiobjective Artificial Bee Colony Algorithm
- Introduction
- Related Work
- Basis of Phylogenetic Inference
- Methods for Inferring Phylogenies
- Multiobjective Artificial Bee Colony
- Artificial Bee Colony Features
- A Multiobjective Artificial Bee Colony Algorithm for Phylogenetic Inference
- Experimental Methodology and Results
- Comparisons with Other Authors
- Conclusions
- References
- Prediction of Mitochondrial Matrix Protein Structures Based on Feature Selection and Fragment Assembly
- Introduction
- Methods
- Representation of Protein Structures
- Construction of Protein Fragments Knowledge Base
- Physico-chemical Feature Selection
- Structure Reconstruction
- Evaluation of Predicted Models
- Experimentation and Results
- Prediction of Mitochondrial Matrix Proteins
- Comparison with RBFNN on the Same Benchmark
- Conclusions and Future Work
- References
- Poster Contributions
- Feature Selection for Lung Cancer Detection Using SVM Based Recursive Feature Elimination Method
- Introduction
- Sample Collection
- Feature Extraction
- Experiments
- Conclusion
- References
- Measuring Gene Expression Noise in Early Drosophila Embryos: The Highly Dynamic Compartmentalized Micro-environment of the Blastoderm Is One of the Main Sources of Noise
- Introduction
- Methods and Approaches
- Immunostaining and Confocal Scanning
- Processing of Sagittal Images and Profile Extraction
- Singular Spectrum Analysis of Expression Profiles
- Estimating the Dependence of the Variance on the Trend
- Results and Discussion
- Photo-Detection Noise
- Can One Distinguish Photomultiplier Tube (PMT) and Residual Noise?
- Texture Noise Character
- Conclusion
- References
- Artificial Immune Systems Perform Valuable Work When Detecting Epistasis in Human Genetic Datasets
- Introduction
- Related Work
- Methods
- AIS Implementation
- Random Search
- Results
- AIS Power
- MDR Comparison
- ROC Analysis
- Discussion and Conclusions
- References
- A Biologically Informed Method for Detecting Associations with Rare Variants
- Introduction
- Paucity of Analytical Tools to Manage Sequence Data
- Biofilter, a Tool to Uncover GxG and GxE Interactions
- Methodology
- Integrate Collapsing Method for Rare Variants Using Biological Knowledge
- Initial Testing
- Application
- Discussion
- Conclusion
- References
- Complex Detection in Protein-Protein Interaction Networks: A Compact Overview for Researchers and Practitioners
- Introduction
- Methods
- Local Neighborhood Density Search (LD)
- Cost-Based Local Search (CL)
- Flow Simulation (FS)
- Statistical Measures (SM)
- Population-Based Stochastic Search (PS)
- Discussion
- Conclusion
- References
- Short-Range Interactions and Decision Tree-Based Protein Contact Map Predictor
- Introduction
- Materials and Methods
- Data Bases
- Contact Maps Definition
- Model Architecture
- The Pre-processing Procedure
- Evaluation of the Efficiency
- Results
- Comparison with the Previous Methods
- Conclusions
- References
- A NSGA-II Algorithm for the Residue-Residue Contact Prediction
- Introduction
- Multi-objective Optimization Problem
- Our Approach
- Encoding
- Fitness Function
- Genetic Operators
- Experiments and Results
- Conclusions and Future Work
- References
- Abstract Contributions
- In Silico Infection of the Human Genome
- Introduction
- The Human Genome
- Computational In Silico Experiment
- No In Silico Evolution?
- Discussion
- References
- Improving Phylogenetic Tree Interpretability by Means of Evolutionary Algorithms
- Short Background in Phylogenetics
- Taxon Ordering in Phylogenetic Trees: A Workbench Test
- Conclusions
- References
- Author Index
