2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008) (eBook)

Title Page 2
Preface 6
Organization 7
Contents 9
Comparing Time Series through Event Clustering 13
Introduction 13
Related Work 15
Proposed Method 16
Results 19
Conclusions 20
References 20
Visual Knowledge-Based Metaphors to Support the Analysis of Polysomnographic Recordings 22
Introduction 22
Prior Definitions 23
Providing Support for the Identification of Apneas and Hypopneas 24
The Algorithm 25
The Visual Metaphor 27
Providing Support for the Identification of Desaturations 27
The Algorithm 28
The Visual Metaphor 29
Experimental Results 29
Discussion 30
Conclusions 31
References 32
A Bio-inspired Proposal for Focus Attention While Preserving Information 33
Introduction: The Problem of Visual Attention 33
Computational Aspects of the Visual Attention Process 34
Layered Computation 34
Presynaptic Inhibition Schemes 35
Convergence and Divergence of Information Process 36
Complete Transforms 36
The Proposed Model: Focus Attention While Preserving Information 37
Conclusions 40
References 40
Modelling Fed-Batch Fermentation Processes: An Approach Based on Artificial Neural Networks 42
Introduction 42
Modelling Fermentation Processes 43
Description of the Computational Tools 44
Methodology 44
White Box Interface 45
Grey Box Interface 46
Case Studies 47
PR Process 47
Ecoli Process 47
Methodology 48
Results 48
PR 48
Ecoli 49
Conclusions and Further Work 50
References 50
New Principles and Adequate Control Methods for Insulin Dosage in Case of Diabetes 52
Introduction 52
New Modelling Concepts for Type I Diabetes 54
Robust Control Methods for Optimal Insulin Dosage in Case of Type I Diabetic Patients 54
Symbolic Computation-Based Robust Algorithms with $Mathematica$ 54
References 55
A Framework for CBR Development and Experimentation with Application to Medical Diagnosis 57
Introduction 57
eXiT*CBR Framework 58
Pre-processing Module 60
Retrieve Module 60
Reuse Module 60
Revise Module 61
Retain Module 61
Experimentation Module 61
Post-processing Module 61
eXiT*CBR Functionalities 62
Application to Breast Cancer Diagnosis 63
Related Work 63
Conclusions 64
References 65
Identification of Relevant Knowledge for Characterizing the Melanoma Domain 67
Introduction 67
Related Work 68
Melanoma Framework 68
Discussion 70
Conclusions and Further Work 70
References 71
TAT-NIDS: An Immune-Based Anomaly Detection Architecture for Network Intrusion Detection 72
Introduction 72
TheTATModel 74
TAT-Based NIDS 74
The Framework 74
The Algorithm 76
Results 77
Conclusions 78
References 78
Novel Computational Methods for Large Scale Genome Comparison 80
Introduction 80
Multiple Genome Alignment of Closely Related Species 81
Local Multiple Alignment of Interspersed Repeats 81
Comparative Genomics Case Study of DUS in $Neisseria$ 82
Conclusion 83
References 84
Improving Literature Searches in Gene Expression Studies 86
Introduction 86
Extracting Knowledge from DNA Microarray Data 87
Proposed Workflow 89
Acquiring, Mapping and Validating Genes Identifiers 89
Using Query Expansion Techniques 90
Searching over PubMed 90
Assembling the Results 91
System Implementation and Avaibility 91
Discussion 92
Conclusion 93
References 93
Implementing an Interactive Web-Based DAS Client 95
Introduction 95
The Distributed Annotation System 96
DASGenExp 96
Implementation 97
The Client 98
The Server 101
Conclusions 102
Future Work 102
References 102
Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of $Zymomonas Mobillis$ 104
Introduction 104
Information Requirements 105
Data Integration 107
Data Source Description 107
Data Quality Issues 108
Integration Strategy 111
Conclusions 112
References 112
Applying CBR Systems to Micro Array Data Classification 114
Introduction 114
CBR System for Classifying Micro Array Data 115
Retrieve 116
Reuse 118
Revise and Retain 119
Case Study 119
Results and Conclusions 120
References 122
Multiple-Microarray Analysis and Internet Gathering Information with Application for Aiding Medical Diagnosis in Cancer Research 124
Introduction 124
Software Architecture 125
Core Functions and Features 126
Co-expression Analysis Module 126
Discriminant Expression Analysis Module 127
Supervised and Unsupervised Clustering Module 127
Net Explorer Module 127
GENECBR Wizard 127
Conclusions 128
References 128
Evolutionary Techniques for Hierarchical Clustering Applied to Microarray Data 130
Introduction 130
The Genetic Algorithm 131
Fitness Function 131
Improving the Fitness Function Cost 133
Mutation Operator 134
Crossover Operator 135
Experiments on Gene Expression Data 135
Goodness of the Individuals 135
Homogeneity, Separation and Agreement with the Reference Partition 136
Conclusion 137
References 138
Beds and Bits: The Challenge of Translational Bioinformatics 140
Introduction 140
Research Lines 141
Microarray Data Analysis 141
Protein Studies 144
Tools 146
Genomic High throughput Studies 146
Protein Studies Tools 146
Conclusions 146
References 147
A Matrix Factorization Classifier for Knowledge-Based Microarray Analysis 149
Introduction 149
The Monocyte - Macrophage Data Set 150
Methods 150
Data Representation and Preprocessing 150
Feature Selection Schemes 151
Matrix Factorization Classifier 152
Discussion 153
Matrix Decomposition Techniques for Feature Selection 153
Matrix Factorization Classifier 156
Conclusion 157
References 157
Named Entity Recognition and Normalization: A Domain-Specific Language Approach 159
Introduction 159
SystemOverview 160
Named Entity Recognition 161
Normalization 162
Evaluation 165
Discussion 166
Availability 166
References 166
BIORED - A Genetic Algorithm for Pattern Detection in Biosequences 168
Introduction 168
Background 169
A Genetic Algorithm for Pattern Discovery in Biosequences 169
Genetic Operators 169
Interestingness Based on Statistical Significance 170
Counting Matches 171
Implementation 172
Performance Evaluation 173
Validation 174
Related Work 174
Conclusion 176
References 176
A Recursive Genetic Algorithm to Automatically Select Genes for Cancer Classification 178
Introduction 178
GASVM-II 179
The Proposed Recursive Genetic Algorithm (R-GA) 181
Experiments 183
Data Sets 183
Experimental Setup 183
Experimental Result 183
Conclusion 185
References 186
On Mining Protein Unfolding Simulation Data with Inductive Logic Programming 187
Introduction 187
ILP in a Nutshell 188
Preliminary Experiments 189
Conclusions and Future Work 190
References 191
A Knowledge Discovery Method for the Characterization of Protein Unfolding Processes 192
Introduction 192
Molecular Dynamics (MD) Protein Unfolding Simulations 193
Simulation Details 193
The Data 194
The Discovery Method 194
Clustering and Data Reduction 195
Event Detection 196
Association Rules 197
Conclusions and Future Work 198
References 199
Design of New Chemoinformatic Tools for the Analysis of Virtual Screening Studies: Application to Tubulin Inhibitors 201
Introduction 201
Docking Results 202
By Hand Clustering 203
Semiautomated Atom Based Attempts to Cluster and Classify the Poses 204
Semiautomated, Interactive, Grid Based Attempts to Cluster and Classify the Poses 205
Conclusions 206
References 207
Multi-Objective Optimization of Biological Networks for Prediction of Intracellular Fluxes 209
Introduction 209
Multi-Objective Flux Balance Analysis (MOFBA) 210
Problem Formulation and Basic Concepts 210
Methods for Multi-Objective Optimization 211
Case Study 211
Results and Discussion 213
Optimization Settings 213
Pareto-Optimal Sets 213
Analysis of Solutions 215
Conclusions 216
References 216
SimSearch: A New Variant of Dynamic Programming Based on Distance Series for Optimal and Near-Optimal Similarity Discovery in Biological Sequences 218
Introduction 218
Related Work 219
Smith-Waterman Algorithm 220
BLAST Algorithm 220
PatternHunter Algorithm 221
The New Algorithm 221
The Similarity Matrices 222
Similarity Discovery 223
The Scoring Scheme 223
Exact Repetitions and Overlapped Patterns 224
Reverse Repetitions 225
Approximate Repetitions 225
Results and Discussion 226
Conclusions 227
References 227
Tuning Parameters of Evolutionary Algorithms Using ROC Analysis 229
Introduction 229
Optimization with Evolutionary Algorithms 230
ROCAnalysis 230
Results 231
Conclusions 233
References 233
Speeding-Up ACO Implementation by Decreasing the Number of Heuristic Function Evaluations in Feature Selection Problem 235
Introduction 235
About ACO and RST 236
Ant Colony Optimization 236
Rough Sets Theory 237
The Hybrid Model Used for Feature Selection (ACO-RST-FS) 238
Improving ACO Runtime 239
Experimental Results 239
Conclusions 242
References 243
Global Sensitivity Analysis of a Biochemical Pathway Model 245
Introduction 245
Global Sensitivity Analysis 246
Sobol’ Global Sensitivity Indices 247
Derivative Based Global Sensitivity Measures 247
Computational Algorithms for Calculation of Integrals 248
Extension to DAEs Systems 250
Results for a Benchmark Pathway 250
Statement of the Problem 250
Results of the Local Sensitivity Analysis 252
Results of the Global Sensitivity Analysis 252
Conclusions 253
References 254
Improving a Leaves Automatic Recognition Process Using PCA 255
Introduction 255
Leaves Database 256
Parameterization System 257
Perimeter Interpolation 257
Reduction Parameters 260
Classification 261
Experiments and Results 261
Conclusions 262
References 263
Author Index 265