Biological computation:
Gespeichert in:
| Hauptverfasser: | , |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Boca Raton, Fla. [u.a.]
CRC Press
2011
|
| Schriftenreihe: | Chapman & Hall/CRC mathematical and computational biology series
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XIX, 323 S. Ill., graph. Darst. |
| ISBN: | 9781420087956 |
Internformat
MARC
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| 245 | 1 | 0 | |a Biological computation |c Ehud Lamm ; Ron Unger |
| 264 | 1 | |a Boca Raton, Fla. [u.a.] |b CRC Press |c 2011 | |
| 300 | |a XIX, 323 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
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| 650 | 0 | 7 | |a Bioinformatik |0 (DE-588)4611085-9 |2 gnd |9 rswk-swf |
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| 999 | |a oai:aleph.bib-bvb.de:BVB01-020197954 | ||
Datensatz im Suchindex
| _version_ | 1804142786893578240 |
|---|---|
| adam_text | Table
of
Contents
Preface,
xv
Chapter
1 ■
Introduction and Biological Background
1.1
BIOLOGICAL COMPUTATION
1
1.2
THE INFLUENCE OF BIOLOGY ON MATHEMATICS-
HISTORICAL EXAMPLES
4
1.3
BIOLOGICAL INTRODUCTION
7
1.3.1
The Cell and Its Activities
12
1.3.2
The Structure of
DNA
14
1.3.3
The Genetic Code
16
1.3.4
Protein Synthesis and Gene Regulation
18
1.3.5
Reproduction and Heredity
23
1.4
MODELS AND SIMULATIONS
26
1.5
SUMMARY
33
1.6
FURTHER READING
34
1.7
EXERCISES
34
1.7.1
Biological Computation
34
1.7.2
History
35
1.7.3
Biological Introduction
35
1.7.4
Models and Simulations
37
1.8
ANSWERS TO SELECTED EXERCISES
37
Chapter
2 ■
Cellular Automata
39
2.1
BIOLOGICAL BACKGROUND
39
vu
viii
■
Table of
Contents
2.1.1
Bacteria
Basics 39
2.1.2
Genetic
Inheritance—Downward and Sideways
40
2.1.3
Diversity and the Species Question
41
2.1.4
Bacteria and Humans
42
2.1.5
The Sociobiology of Bacteria
42
2.2
THE GAME OF LIFE
44
2.3
GENERAL DEFINITION OF CELLULAR AUTOMATA
48
2.4 1
-DIMENSIONAL AUTOMATA
50
2.5
EXAMPLES OF CELLULAR AUTOMATA
54
2.5.1
Fur Color
54
2.5.2
Ecological Models
57
2.5.3
Food Chain
58
2.6
COMPARISON WITH A CONTINUOUS
MATHEMATICAL MODEL
59
2.7
COMPUTATIONAL UNIVERSALITY
61
2.7.1
What Is Universality?
61
2.7.2
Cellular Automata as a Computational Model
65
2.7.3
How to Prove That a CA Is Universal
67
2.7.4
Universality of a Two-Dimensional Cellular
Automaton
—
Proof Sketch
68
2.7.5
Universality of the Game of Life —Proof Sketch
71
2.8
SELF-REPLICATION
73
2.9
SUMMARY
77
2.10
PSEUDO-CODE
78
2.11
FURTHER READING
79
2.12
EXERCISES
79
2.12.1
Game of Life
79
2.12.2
Cellular Automata
80
2.12.3
Computing Using Cellular Automata
82
2.12.4
Self-Replication
82
2.12.5
Programming Exercises
83
Table
of Contents
■ ix
2.13
ANSWERS TO SELECTED EXERCISES
84
Chapter
3 ■
Evolutionary Computation
___________________87
3.1
EVOLUTIONARY BIOLOGY AND EVOLUTIONARY
COMPUTATION
87
3.1.1
Natural Selection
87
3.1.2
Evolutionary Computation
93
3.2
GENETIC ALGORITHMS
94
3.2.1
Selection and Fitness
98
3.2.2
Variations on Fitness Functions
102
3.2.3
Genetic Operators and the Representation of
Solutions
104
3.3
EXAMPLE APPLICATIONS
108
3.3.1
Scheduling
108
3.3.2
Engineering Optimization
109
3.3.3
Pattern Recognition and Classification
109
3.3.4
Designing Cellular Automata
110
3.3.5
Designing Neural Networks
110
3.3.6
Bioinformatics
110
3.4
ANALYSIS OF THE BEHAVIOR OF GENETIC
ALGORITHMS
111
3.4.1
Holland s Building Blocks Hypothesis
115
3.4.2
The Schema Theorem
116
3.4.3
Corollaries of the Schema Theorem
118
3.5
LAMARCKIAN EVOLUTION
119
3.6
GENETIC PROGRAMMING
121
3.7
A SECOND LOOK AT THE EVOLUTIONARY PROCESS
126
3.7.1
Mechanisms for the Generation and Inheritance of
Variations
126
3.7.2
Selection
129
3.8
SUMMARY
130
3.9
PSEUDO-CODE
131
3.10
FURTHER READING
132
χ
■
Table of Contents
3.11
EXERCISES
132
3.11.1
Evolutionary Computation
132
3.11.2
Genetic Algorithms
133
3.11.3
Selection and Fitness
133
3.11.4
Genetic Operators and the Representation of
Solutions
134
3.11.5
Analysis of the Behavior of Genetic Algorithms
135
3.11.6
Genetic Programming
136
3.11.7
Programming Exercises
136
3.12
ANSWERS TO SELECTED EXERCISES
140
Chapter
4 ■
Artificial Neural Networks
_________________143
4.1
BIOLOGICAL BACKGROUND
143
4.1.1
Neural Networks as Computational Model
146
4.2
LEARNING
146
4.3
ARTIFICIAL NEURAL NETWORKS
148
4.3.1
General Structure of Artificial Neural Networks
148
4.3.2
Training an Artificial Neural Network
151
4.4
THE PERCEPTRON
152
4.4.1
Definition of a Perceptron
152
4.4.2
Formal Description of the Behavior of a Perceptron
156
4.4.3
The Perceptron Learning Rule
158
4.4.4
Proving the Convergence of the Perceptron
Learning Algorithm
159
4.5
LEARNING IN A MULTILAYERED NETWORK
162
4.5.1
The Backpropagation Algorithm
162
4.5.2
Analysis of Learning Algorithms
170
4.5.3
Network Design
172
4.5.4
Examples of Applications
174
4.6
ASSOCIATIVE MEMORY
180
4.6.1
Biological Memory
180
4.6.2
Hopfield Networks
181
Table
of Contents
■ xi
4.6.3
Memorization in a Hopfield Network
181
4.6.4
Data Retrieval in a Hopfield Network
183
4.6.5
The Convergence of the Process of Updating the
Neurons
185
4.6.6
Analyzing the Capacity of a Hopfield Network
186
4.6.7
Application of a Hopfield Network
189
4.6.8
Further Uses of the Hopfield Network
191
4.7
UNSUPERVISED LEARNING
194
4.7.1
Self-Organizing Maps
195
4.7.2
WEBSOM: Example of Using SOMs for Document
Text Mining
198
4.8
SUMMARY
200
4.9
FURTHER READING
201
4.10
EXERCISES
202
4.10.1
Single-Layer Perceptrons
202
4.10.2
Multilayer Networks
203
4.10.3
Hopfield Networks
205
4.10.4
Self-Organizing Maps
208
4.10.5
Summary
208
4.11
ANSWERS TO SELECTED EXERCISES
210
Chapter
5
ш
Molecular Computation
_____________________21 5
5.1
BIOLOGICAL BACKGROUND
217
5.1.1
PCR: Polymerase Chain Reaction
217
5.1.2
Gel Electrophoresis
219
5.1.3
Restriction Enzymes
219
5.1.4
Ligation
220
5.2
COMPUTATION USING
DNA 220
5.2.1
Hamiltonian Paths
220
5.2.2
Solving SAT
230
5.2.3 DNA
Tiling
233
5.2.4 DNA
Computing—Summary
236
xii ■
Table
of Contents
5.3
ENZYMATIC COMPUTATION
237
5.3.1
Finite Automata
238
5.3.2
Enzymatic Implementation of Finite Automata
242
5.4
SUMMARY
248
5.5
FURTHER READING
250
5.6
EXERCISES
250
5.6.1
Biological Background
250
5.6.2
Computing with
DNA 250
5.6.3
Enzymatic Computation
253
5.7
ANSWERS TO SELECTED EXERCISES
254
Chapter
б
■
The Never-Ending Story: Additional Topics
at the Interface between Biology and
Computation
259
6.1
SWARM INTELLIGENCE
261
6.1.1
Ant Colony Optimization Algorithms
262
6.1.2
Cemetery Organization, Larval Sorting, and
Clustering
264
6.1.3
Particle Swarm Optimization
267
6.2
ARTIFICIAL IMMUNE SYSTEMS
270
6.2.1
Identifying Intrusions in a Computer Network
271
6.3
ARTIFICIAL LIFE
273
6.3.1
Avida
276
6.3.2
Evolvable Virtual Creatures
281
6.4
SYSTEMS BIOLOGY
284
6.4.1
Evolution of Modularity
287
6.4.2
Robustness of Biological Systems
289
6.4.3
Formal Languages for Describing Biological
Systems
290
6.5
SUMMARY
294
6.6
RECOMMENDATIONS FOR ADDITIONAL READING
297
6.6.1
Biological Introduction
297
Table
of Contents
■ xiii
6.6.2
Personal Perspectives
298
6.6.3
Modeling Biological Systems
298
6.6.4
Biological Computation
299
6.6.5
Cellular Automata
299
6.6.6
Evolutionary Computation
300
6.6.7
Neural Networks
300
6.6.8
Molecular Computation
300
6.6.9
Swarm Intelligence
300
6.6.10
Systems Biology
301
6.6.11
Bioinformatics
301
6.7
FURTHER READING
301
6.8
EXERCISES
302
6.8.1
Swarm Intelligence
302
6.8.2
Artificial Immune Systems
303
6.8.3
Artificial Life
305
6.8.4
Systems Biology
306
6.8.5
Programming Exercises
306
6.9
ANSWERS TO SELECTED EXERCISES
307
INDEX,
311
|
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| id | DE-604.BV025602678 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T22:37:18Z |
| institution | BVB |
| isbn | 9781420087956 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-020197954 |
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| spelling | Lamm, Ehud Verfasser (DE-588)1013050428 aut Biological computation Ehud Lamm ; Ron Unger Boca Raton, Fla. [u.a.] CRC Press 2011 XIX, 323 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Chapman & Hall/CRC mathematical and computational biology series Bioinformatik (DE-588)4611085-9 gnd rswk-swf Bioinformatik (DE-588)4611085-9 s DE-604 Unger, Ron 1958- Verfasser (DE-588)1013050436 aut Digitalisierung UB Bamberg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020197954&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Lamm, Ehud Unger, Ron 1958- Biological computation Bioinformatik (DE-588)4611085-9 gnd |
| subject_GND | (DE-588)4611085-9 |
| title | Biological computation |
| title_auth | Biological computation |
| title_exact_search | Biological computation |
| title_full | Biological computation Ehud Lamm ; Ron Unger |
| title_fullStr | Biological computation Ehud Lamm ; Ron Unger |
| title_full_unstemmed | Biological computation Ehud Lamm ; Ron Unger |
| title_short | Biological computation |
| title_sort | biological computation |
| topic | Bioinformatik (DE-588)4611085-9 gnd |
| topic_facet | Bioinformatik |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020197954&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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