Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics

Name: Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics | 10th European Conference, EvoBIO 2012, Málaga, Spain, April 11-13, 2012, Proceedings
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10th European Conference, EvoBIO 2012, Málaga, Spain, April 11-13, 2012, Proceedings

Mario Giacobini Leonardo Vanneschi William S. Bush(Herausgeber*in)

Springer (Verlag)

Erschienen am 23. März 2012

XIII, 255 Seiten

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Inhalt

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

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