Neural networks and genome informatics:
Gespeichert in:
| Hauptverfasser: | , |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Amsterdam [u.a.]
Elsevier
2000
|
| Ausgabe: | 1. ed. |
| Schriftenreihe: | Methods in computational biology and biochemistry
1 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | 205 S. graph. Darst. |
| ISBN: | 0080428002 |
Internformat
MARC
| LEADER | 00000nam a2200000 cb4500 | ||
|---|---|---|---|
| 001 | BV013915030 | ||
| 003 | DE-604 | ||
| 005 | 20011126 | ||
| 007 | t | ||
| 008 | 010917s2000 d||| |||| 00||| eng d | ||
| 020 | |a 0080428002 |9 0-08-042800-2 | ||
| 035 | |a (OCoLC)489044920 | ||
| 035 | |a (DE-599)BVBBV013915030 | ||
| 040 | |a DE-604 |b ger |e rakwb | ||
| 041 | 0 | |a eng | |
| 049 | |a DE-355 |a DE-91G |a DE-526 |a DE-B768 | ||
| 082 | 0 | |a 576.50285632 |2 21 | |
| 084 | |a ST 152 |0 (DE-625)143596: |2 rvk | ||
| 084 | |a DAT 717f |2 stub | ||
| 100 | 1 | |a Wu, Cathy H. |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Neural networks and genome informatics |c C. H. Wu ; J. W. McLarty |
| 250 | |a 1. ed. | ||
| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier |c 2000 | |
| 300 | |a 205 S. |b graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 1 | |a Methods in computational biology and biochemistry |v 1 | |
| 650 | 4 | |a Bioinformatics | |
| 650 | 4 | |a Genetics - Data processing | |
| 650 | 4 | |a Genomes | |
| 650 | 4 | |a Neural networks (Computer science) | |
| 650 | 0 | 7 | |a Genom |0 (DE-588)4156640-3 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Neuronales Netz |0 (DE-588)4226127-2 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Bioinformatik |0 (DE-588)4611085-9 |2 gnd |9 rswk-swf |
| 689 | 0 | 0 | |a Neuronales Netz |0 (DE-588)4226127-2 |D s |
| 689 | 0 | 1 | |a Genom |0 (DE-588)4156640-3 |D s |
| 689 | 0 | |5 DE-604 | |
| 689 | 1 | 0 | |a Genom |0 (DE-588)4156640-3 |D s |
| 689 | 1 | 1 | |a Bioinformatik |0 (DE-588)4611085-9 |D s |
| 689 | 1 | 2 | |a Neuronales Netz |0 (DE-588)4226127-2 |D s |
| 689 | 1 | |5 DE-604 | |
| 700 | 1 | |a MacLarty, Jerry W. |e Verfasser |4 aut | |
| 830 | 0 | |a Methods in computational biology and biochemistry |v 1 |w (DE-604)BV013959856 |9 1 | |
| 856 | 4 | 2 | |m HEBIS Datenaustausch |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009520941&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 999 | |a oai:aleph.bib-bvb.de:BVB01-009520941 | ||
Datensatz im Suchindex
| _version_ | 1804128758008905728 |
|---|---|
| adam_text | Neural Networks and
Genome Informatics
CH Wu
J W McLarty
University of Texas Health Center at Tyler
Department of Epidemiology and Biomathematics
11937 U S Highway 271
Tyler, TX 75708-3154
USA
ELSEVIER
Amsterdam - Lausanne - New York - Oxford - Shannon - Singapore - Tokyo
Contents
PARTI 1
Overview 1
CHAPTER 1 3
Neural Networks for Genome Informatics 3
1 1 What Is Genome Informatics? 3
111 Gene Recognition and DNA Sequence Analysis 4
112 Protein Structure Prediction 8
113 Protein Family Classification and Sequence Analysis 9
1 2 What Is An Artificial Neural Network? 10
1 3 Genome Informatics Applications 11
1 4 References 12
PART II 17
Neural Network Foundations 17
CHAPTER 2 19
Neural Network Basics 19
2 1 Introduction to Neural Network Elements 19
211 Neurons 19
212 Connections between Elements 20
2 2 Transfer Functions 21
231 Summation Operation 21
232 Thresholding Functions 22
233 Other Transfer Functions 24
2 4 Simple Feed-Forward Network Example 25
2 5 Introductory Texts 26
2 6 References 27
CHAPTER 3 29
Perceptions and Multilayer Perceptrons 29
3 1Perceptrons 29
311 Applications 29
312 Limitations 33
3 2 Multilayer Perceptrons 33
321 Applications 36
322 Limitations 38
3 3 References 38
CHAPTER 4 41
Other Common Architectures 41
4 1 Radial Basis Functions 41
411 Introduction to Radial Basis Functions 41
412 Applications 44
413 Limitations 46
4 2 Kohonen Self-organizing Maps 46
421 Background 47
422 Applications 48
423 Limitations 50
4 4 References 50
CHAPTERS 51
Training of Neural Networks 51
5 1 Supervised Learning 51
521 Training Perceptrons 52
522 Multilayer Perceptrons 55
523 Radial Basis Functions 58
524 Supervised Training Issues 59
5 3 Unsupervised Learning 62
5 4 Software for Training Neural Networks 63
5 5 References 63
PART HI 65
Genome Informatics Applications 65
CHAPTERS , 67
Design Issues - Feature Presentation 67
6 1 Overview of Design Issues 67
6 2 Amino Acid Residues 68
6 3 Amino Acid Physicochemical and Structural Features 69
6 4 Protein Context Features and Domains 71
6 5 Protein Evolutionary Features 73
6 6 Feature Representation 74
6 7 References 76
CHAPTER 7 79
Design Issues - Data Encoding 79
7 1 Direct Input Sequence Encoding 79
7 2 Indirect Input Sequence Encoding 81
7 3 Construction of Input Layer 83
7 4 Input Trimming 84
7 5 Output Encoding 86
7 6 References 86
CHAPTER 8 89
Design Issues - Neural Networks 89
8 1 Network Architecture 89
8 2 Network Learning Algorithm 91
8 3 Network Parameters 92
8 4 Training and Test Data 94
841 Network Generalization 94
842 Data Quality and Quantity 95
843 Benchmarking Data Set 96
8 5 Evaluation Mechanism 97
8 6 References 99
CHAPTER 9 103
Applications - Nucleic Acid Sequence Analysis 103
9 1 Introduction 103
9 2 Coding Region Recognition and Gene Identification 105
9 3 Recognition of Transcriptional and Translational Signals 107
9 4 Sequence Feature Analysis and Classification 110
9 5 References I l l
CHAPTER 10 115
Applications - Protein Structure Prediction 115
10 1 Introduction 116
10 2 Protein Secondary Structure Prediction 116
10 3 Protein Tertiary Structure Prediction 121
Protein Distance Constraints 123
10 4 Protein Folding Class Prediction 123
10 5 References 125
CHAPTER 11 129
Applications - Protein Sequence Analysis 129
11 1 Introduction 129
11 2 Signal Peptide Prediction 130
11 3 Other Motif Region and Site Prediction 133
11 4 Protein Family Classification 136
11 5 References 140
Part IV 143
Open Problems and Future Directions 143
CHAPTER 12 145
Integration of Statistical Methods into Neural Network Applications 145
12 1 Problems in Model Development 146
12 1 1 Input Variable Selection 146
12 1 2 Number of Hidden Layers and Units 147
12 1 3 Comparison of Architectures 147
12 1 4 Need for Benchmark Data 148
12 2 Training Issues 148
12 3 Interpretation of Results 149
12 4 Further Sources of Information 149
12 5 References 149
CHAPTER 13 152
Future of Genome Informatics Applications 152
13 1 Rule and Feature Extraction from Neural Networks 152
13 2 1 Rule Extraction from Pruned Networks 152
13 2 2 Feature Extraction by Measuring Importance of Inputs 153
13 2 3 Feature Extraction Based on Variable Selection 154
13 2 4 Network Understanding Based on Output Interpretation 155
13 2 Neural Network Design Using Prior Knowledge 156
13 3 Conclusions 157
13 4 References 158
Glossary 161
Author Index 193
Subject Index 201
|
| any_adam_object | 1 |
| author | Wu, Cathy H. MacLarty, Jerry W. |
| author_facet | Wu, Cathy H. MacLarty, Jerry W. |
| author_role | aut aut |
| author_sort | Wu, Cathy H. |
| author_variant | c h w ch chw j w m jw jwm |
| building | Verbundindex |
| bvnumber | BV013915030 |
| classification_rvk | ST 152 |
| classification_tum | DAT 717f |
| ctrlnum | (OCoLC)489044920 (DE-599)BVBBV013915030 |
| dewey-full | 576.50285632 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 576 - Genetics and evolution |
| dewey-raw | 576.50285632 |
| dewey-search | 576.50285632 |
| dewey-sort | 3576.50285632 |
| dewey-tens | 570 - Biology |
| discipline | Biologie Informatik |
| edition | 1. ed. |
| format | Book |
| fullrecord | <?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>01960nam a2200517 cb4500</leader><controlfield tag="001">BV013915030</controlfield><controlfield tag="003">DE-604</controlfield><controlfield tag="005">20011126 </controlfield><controlfield tag="007">t</controlfield><controlfield tag="008">010917s2000 d||| |||| 00||| eng d</controlfield><datafield tag="020" ind1=" " ind2=" "><subfield code="a">0080428002</subfield><subfield code="9">0-08-042800-2</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(OCoLC)489044920</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-599)BVBBV013915030</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-604</subfield><subfield code="b">ger</subfield><subfield code="e">rakwb</subfield></datafield><datafield tag="041" ind1="0" ind2=" "><subfield code="a">eng</subfield></datafield><datafield tag="049" ind1=" " ind2=" "><subfield code="a">DE-355</subfield><subfield code="a">DE-91G</subfield><subfield code="a">DE-526</subfield><subfield code="a">DE-B768</subfield></datafield><datafield tag="082" ind1="0" ind2=" "><subfield code="a">576.50285632</subfield><subfield code="2">21</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">ST 152</subfield><subfield code="0">(DE-625)143596:</subfield><subfield code="2">rvk</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">DAT 717f</subfield><subfield code="2">stub</subfield></datafield><datafield tag="100" ind1="1" ind2=" "><subfield code="a">Wu, Cathy H.</subfield><subfield code="e">Verfasser</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Neural networks and genome informatics</subfield><subfield code="c">C. H. Wu ; J. W. McLarty</subfield></datafield><datafield tag="250" ind1=" " ind2=" "><subfield code="a">1. ed.</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="a">Amsterdam [u.a.]</subfield><subfield code="b">Elsevier</subfield><subfield code="c">2000</subfield></datafield><datafield tag="300" ind1=" " ind2=" "><subfield code="a">205 S.</subfield><subfield code="b">graph. Darst.</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="b">n</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="b">nc</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="490" ind1="1" ind2=" "><subfield code="a">Methods in computational biology and biochemistry</subfield><subfield code="v">1</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Bioinformatics</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Genetics - Data processing</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Genomes</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Neural networks (Computer science)</subfield></datafield><datafield tag="650" ind1="0" ind2="7"><subfield code="a">Genom</subfield><subfield code="0">(DE-588)4156640-3</subfield><subfield code="2">gnd</subfield><subfield code="9">rswk-swf</subfield></datafield><datafield tag="650" ind1="0" ind2="7"><subfield code="a">Neuronales Netz</subfield><subfield code="0">(DE-588)4226127-2</subfield><subfield code="2">gnd</subfield><subfield code="9">rswk-swf</subfield></datafield><datafield tag="650" ind1="0" ind2="7"><subfield code="a">Bioinformatik</subfield><subfield code="0">(DE-588)4611085-9</subfield><subfield code="2">gnd</subfield><subfield code="9">rswk-swf</subfield></datafield><datafield tag="689" ind1="0" ind2="0"><subfield code="a">Neuronales Netz</subfield><subfield code="0">(DE-588)4226127-2</subfield><subfield code="D">s</subfield></datafield><datafield tag="689" ind1="0" ind2="1"><subfield code="a">Genom</subfield><subfield code="0">(DE-588)4156640-3</subfield><subfield code="D">s</subfield></datafield><datafield tag="689" ind1="0" ind2=" "><subfield code="5">DE-604</subfield></datafield><datafield tag="689" ind1="1" ind2="0"><subfield code="a">Genom</subfield><subfield code="0">(DE-588)4156640-3</subfield><subfield code="D">s</subfield></datafield><datafield tag="689" ind1="1" ind2="1"><subfield code="a">Bioinformatik</subfield><subfield code="0">(DE-588)4611085-9</subfield><subfield code="D">s</subfield></datafield><datafield tag="689" ind1="1" ind2="2"><subfield code="a">Neuronales Netz</subfield><subfield code="0">(DE-588)4226127-2</subfield><subfield code="D">s</subfield></datafield><datafield tag="689" ind1="1" ind2=" "><subfield code="5">DE-604</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">MacLarty, Jerry W.</subfield><subfield code="e">Verfasser</subfield><subfield code="4">aut</subfield></datafield><datafield tag="830" ind1=" " ind2="0"><subfield code="a">Methods in computational biology and biochemistry</subfield><subfield code="v">1</subfield><subfield code="w">(DE-604)BV013959856</subfield><subfield code="9">1</subfield></datafield><datafield tag="856" ind1="4" ind2="2"><subfield code="m">HEBIS Datenaustausch</subfield><subfield code="q">application/pdf</subfield><subfield code="u">http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009520941&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA</subfield><subfield code="3">Inhaltsverzeichnis</subfield></datafield><datafield tag="999" ind1=" " ind2=" "><subfield code="a">oai:aleph.bib-bvb.de:BVB01-009520941</subfield></datafield></record></collection> |
| id | DE-604.BV013915030 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T18:54:19Z |
| institution | BVB |
| isbn | 0080428002 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-009520941 |
| oclc_num | 489044920 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR DE-91G DE-BY-TUM DE-526 DE-B768 |
| owner_facet | DE-355 DE-BY-UBR DE-91G DE-BY-TUM DE-526 DE-B768 |
| physical | 205 S. graph. Darst. |
| publishDate | 2000 |
| publishDateSearch | 2000 |
| publishDateSort | 2000 |
| publisher | Elsevier |
| record_format | marc |
| series | Methods in computational biology and biochemistry |
| series2 | Methods in computational biology and biochemistry |
| spelling | Wu, Cathy H. Verfasser aut Neural networks and genome informatics C. H. Wu ; J. W. McLarty 1. ed. Amsterdam [u.a.] Elsevier 2000 205 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in computational biology and biochemistry 1 Bioinformatics Genetics - Data processing Genomes Neural networks (Computer science) Genom (DE-588)4156640-3 gnd rswk-swf Neuronales Netz (DE-588)4226127-2 gnd rswk-swf Bioinformatik (DE-588)4611085-9 gnd rswk-swf Neuronales Netz (DE-588)4226127-2 s Genom (DE-588)4156640-3 s DE-604 Bioinformatik (DE-588)4611085-9 s MacLarty, Jerry W. Verfasser aut Methods in computational biology and biochemistry 1 (DE-604)BV013959856 1 HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009520941&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Wu, Cathy H. MacLarty, Jerry W. Neural networks and genome informatics Methods in computational biology and biochemistry Bioinformatics Genetics - Data processing Genomes Neural networks (Computer science) Genom (DE-588)4156640-3 gnd Neuronales Netz (DE-588)4226127-2 gnd Bioinformatik (DE-588)4611085-9 gnd |
| subject_GND | (DE-588)4156640-3 (DE-588)4226127-2 (DE-588)4611085-9 |
| title | Neural networks and genome informatics |
| title_auth | Neural networks and genome informatics |
| title_exact_search | Neural networks and genome informatics |
| title_full | Neural networks and genome informatics C. H. Wu ; J. W. McLarty |
| title_fullStr | Neural networks and genome informatics C. H. Wu ; J. W. McLarty |
| title_full_unstemmed | Neural networks and genome informatics C. H. Wu ; J. W. McLarty |
| title_short | Neural networks and genome informatics |
| title_sort | neural networks and genome informatics |
| topic | Bioinformatics Genetics - Data processing Genomes Neural networks (Computer science) Genom (DE-588)4156640-3 gnd Neuronales Netz (DE-588)4226127-2 gnd Bioinformatik (DE-588)4611085-9 gnd |
| topic_facet | Bioinformatics Genetics - Data processing Genomes Neural networks (Computer science) Genom Neuronales Netz Bioinformatik |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=009520941&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV013959856 |
| work_keys_str_mv | AT wucathyh neuralnetworksandgenomeinformatics AT maclartyjerryw neuralnetworksandgenomeinformatics |