Parameter Synthesis and Robustness Analysis of Rule-Based Models View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2020-08-10

AUTHORS

Matej Troják , David Šafránek , Lukrécia Mertová , Luboš Brim

ABSTRACT

We introduce the Quantitative Biochemical Space Language, a rule-based language for a compact modelling of probabilistic behaviour of complex parameter-dependent biological systems. Application of rules is governed by an associated parametrised rate function, expressing partially known information about the behaviour of the modelled system. The parameter values influence the behaviour of the model. We propose a formal verification-based method for the synthesis of parameter values (parameter synthesis) which ensure the behaviour of the modelled system satisfies a given PCTL property. In addition, we demonstrate how this method can be used for robustness analysis. More... »

PAGES

41-59

Book

TITLE

NASA Formal Methods

ISBN

978-3-030-55753-9
978-3-030-55754-6

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-3-030-55754-6_3

DOI

http://dx.doi.org/10.1007/978-3-030-55754-6_3

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1130001539


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/08", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Information and Computing Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0801", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Artificial Intelligence and Image Processing", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Systems Biology Laboratory, Masaryk University, Brno, Czech Republic", 
          "id": "http://www.grid.ac/institutes/grid.10267.32", 
          "name": [
            "Systems Biology Laboratory, Masaryk University, Brno, Czech Republic"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Troj\u00e1k", 
        "givenName": "Matej", 
        "id": "sg:person.013614147255.44", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013614147255.44"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Systems Biology Laboratory, Masaryk University, Brno, Czech Republic", 
          "id": "http://www.grid.ac/institutes/grid.10267.32", 
          "name": [
            "Systems Biology Laboratory, Masaryk University, Brno, Czech Republic"
          ], 
          "type": "Organization"
        }, 
        "familyName": "\u0160afr\u00e1nek", 
        "givenName": "David", 
        "id": "sg:person.011410250615.43", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011410250615.43"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Systems Biology Laboratory, Masaryk University, Brno, Czech Republic", 
          "id": "http://www.grid.ac/institutes/grid.10267.32", 
          "name": [
            "Systems Biology Laboratory, Masaryk University, Brno, Czech Republic"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mertov\u00e1", 
        "givenName": "Lukr\u00e9cia", 
        "id": "sg:person.012266350607.01", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012266350607.01"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Systems Biology Laboratory, Masaryk University, Brno, Czech Republic", 
          "id": "http://www.grid.ac/institutes/grid.10267.32", 
          "name": [
            "Systems Biology Laboratory, Masaryk University, Brno, Czech Republic"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Brim", 
        "givenName": "Lubo\u0161", 
        "id": "sg:person.0645117057.83", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0645117057.83"
        ], 
        "type": "Person"
      }
    ], 
    "datePublished": "2020-08-10", 
    "datePublishedReg": "2020-08-10", 
    "description": "We introduce the Quantitative Biochemical Space Language, a rule-based language for a compact modelling of probabilistic behaviour of complex parameter-dependent biological systems. Application of rules is governed by an associated parametrised rate function, expressing partially known information about the behaviour of the modelled system. The parameter values influence the behaviour of the model. We propose a formal verification-based method for the synthesis of parameter values (parameter synthesis) which ensure the behaviour of the modelled system satisfies a given PCTL property. In addition, we demonstrate how this method can be used for robustness analysis.", 
    "editor": [
      {
        "familyName": "Lee", 
        "givenName": "Ritchie", 
        "type": "Person"
      }, 
      {
        "familyName": "Jha", 
        "givenName": "Susmit", 
        "type": "Person"
      }, 
      {
        "familyName": "Mavridou", 
        "givenName": "Anastasia", 
        "type": "Person"
      }, 
      {
        "familyName": "Giannakopoulou", 
        "givenName": "Dimitra", 
        "type": "Person"
      }
    ], 
    "genre": "chapter", 
    "id": "sg:pub.10.1007/978-3-030-55754-6_3", 
    "inLanguage": "en", 
    "isAccessibleForFree": false, 
    "isPartOf": {
      "isbn": [
        "978-3-030-55753-9", 
        "978-3-030-55754-6"
      ], 
      "name": "NASA Formal Methods", 
      "type": "Book"
    }, 
    "keywords": [
      "robustness analysis", 
      "parameter values", 
      "compact modelling", 
      "parameter synthesis", 
      "rate function", 
      "probabilistic behavior", 
      "PCTL properties", 
      "biological systems", 
      "model", 
      "space languages", 
      "system", 
      "modelling", 
      "rules", 
      "behavior", 
      "properties", 
      "applications", 
      "function", 
      "values", 
      "application of rules", 
      "analysis", 
      "rule-based language", 
      "information", 
      "addition", 
      "language", 
      "synthesis", 
      "method"
    ], 
    "name": "Parameter Synthesis and Robustness Analysis of Rule-Based Models", 
    "pagination": "41-59", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1130001539"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/978-3-030-55754-6_3"
        ]
      }
    ], 
    "publisher": {
      "name": "Springer Nature", 
      "type": "Organisation"
    }, 
    "sameAs": [
      "https://doi.org/10.1007/978-3-030-55754-6_3", 
      "https://app.dimensions.ai/details/publication/pub.1130001539"
    ], 
    "sdDataset": "chapters", 
    "sdDatePublished": "2022-05-10T10:55", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20220509/entities/gbq_results/chapter/chapter_72.jsonl", 
    "type": "Chapter", 
    "url": "https://doi.org/10.1007/978-3-030-55754-6_3"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/978-3-030-55754-6_3'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/978-3-030-55754-6_3'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/978-3-030-55754-6_3'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/978-3-030-55754-6_3'


 

This table displays all metadata directly associated to this object as RDF triples.

122 TRIPLES      23 PREDICATES      51 URIs      44 LITERALS      7 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/978-3-030-55754-6_3 schema:about anzsrc-for:08
2 anzsrc-for:0801
3 schema:author N306ba1d7a2864cc9a7d6424a368fa58f
4 schema:datePublished 2020-08-10
5 schema:datePublishedReg 2020-08-10
6 schema:description We introduce the Quantitative Biochemical Space Language, a rule-based language for a compact modelling of probabilistic behaviour of complex parameter-dependent biological systems. Application of rules is governed by an associated parametrised rate function, expressing partially known information about the behaviour of the modelled system. The parameter values influence the behaviour of the model. We propose a formal verification-based method for the synthesis of parameter values (parameter synthesis) which ensure the behaviour of the modelled system satisfies a given PCTL property. In addition, we demonstrate how this method can be used for robustness analysis.
7 schema:editor N4bd356c87a684ed7a844c24988663fca
8 schema:genre chapter
9 schema:inLanguage en
10 schema:isAccessibleForFree false
11 schema:isPartOf N8c6d96abd62a457382c3a4a72863ad8d
12 schema:keywords PCTL properties
13 addition
14 analysis
15 application of rules
16 applications
17 behavior
18 biological systems
19 compact modelling
20 function
21 information
22 language
23 method
24 model
25 modelling
26 parameter synthesis
27 parameter values
28 probabilistic behavior
29 properties
30 rate function
31 robustness analysis
32 rule-based language
33 rules
34 space languages
35 synthesis
36 system
37 values
38 schema:name Parameter Synthesis and Robustness Analysis of Rule-Based Models
39 schema:pagination 41-59
40 schema:productId N485045bb2f0f4419ba8fa13273ffa0e8
41 Nfc4823f97fae419288405525b9998974
42 schema:publisher N2a8c7a16b26f43208a4466c41735f64f
43 schema:sameAs https://app.dimensions.ai/details/publication/pub.1130001539
44 https://doi.org/10.1007/978-3-030-55754-6_3
45 schema:sdDatePublished 2022-05-10T10:55
46 schema:sdLicense https://scigraph.springernature.com/explorer/license/
47 schema:sdPublisher Nf2aa971e93c147f6bc5f7e4984d5cb8f
48 schema:url https://doi.org/10.1007/978-3-030-55754-6_3
49 sgo:license sg:explorer/license/
50 sgo:sdDataset chapters
51 rdf:type schema:Chapter
52 N2a8c7a16b26f43208a4466c41735f64f schema:name Springer Nature
53 rdf:type schema:Organisation
54 N306ba1d7a2864cc9a7d6424a368fa58f rdf:first sg:person.013614147255.44
55 rdf:rest Nf51c1ee5166645a1a960c3d653ce4c58
56 N37ba9fd14be74f2cbf5db3fb909cc600 schema:familyName Mavridou
57 schema:givenName Anastasia
58 rdf:type schema:Person
59 N469998beaf3a4dd0887d5c18b702ea5e rdf:first sg:person.0645117057.83
60 rdf:rest rdf:nil
61 N485045bb2f0f4419ba8fa13273ffa0e8 schema:name doi
62 schema:value 10.1007/978-3-030-55754-6_3
63 rdf:type schema:PropertyValue
64 N4bd356c87a684ed7a844c24988663fca rdf:first N72573bcec95249cf83ba5d16d2cc5b3b
65 rdf:rest Ndd02afed450c40bf93ec4c417542bc59
66 N5bf2444a88704964a8822e025854d72c rdf:first N37ba9fd14be74f2cbf5db3fb909cc600
67 rdf:rest Nd67be2de05124b5aa28c2baa4b9af48c
68 N72573bcec95249cf83ba5d16d2cc5b3b schema:familyName Lee
69 schema:givenName Ritchie
70 rdf:type schema:Person
71 N8c6d96abd62a457382c3a4a72863ad8d schema:isbn 978-3-030-55753-9
72 978-3-030-55754-6
73 schema:name NASA Formal Methods
74 rdf:type schema:Book
75 Na691a2d6548b41458e58cbce33a342e8 schema:familyName Jha
76 schema:givenName Susmit
77 rdf:type schema:Person
78 Nacc1496302984f6cb93e21d06646f408 schema:familyName Giannakopoulou
79 schema:givenName Dimitra
80 rdf:type schema:Person
81 Nd143a0b6a14241d38e4cd773f98204b4 rdf:first sg:person.012266350607.01
82 rdf:rest N469998beaf3a4dd0887d5c18b702ea5e
83 Nd67be2de05124b5aa28c2baa4b9af48c rdf:first Nacc1496302984f6cb93e21d06646f408
84 rdf:rest rdf:nil
85 Ndd02afed450c40bf93ec4c417542bc59 rdf:first Na691a2d6548b41458e58cbce33a342e8
86 rdf:rest N5bf2444a88704964a8822e025854d72c
87 Nf2aa971e93c147f6bc5f7e4984d5cb8f schema:name Springer Nature - SN SciGraph project
88 rdf:type schema:Organization
89 Nf51c1ee5166645a1a960c3d653ce4c58 rdf:first sg:person.011410250615.43
90 rdf:rest Nd143a0b6a14241d38e4cd773f98204b4
91 Nfc4823f97fae419288405525b9998974 schema:name dimensions_id
92 schema:value pub.1130001539
93 rdf:type schema:PropertyValue
94 anzsrc-for:08 schema:inDefinedTermSet anzsrc-for:
95 schema:name Information and Computing Sciences
96 rdf:type schema:DefinedTerm
97 anzsrc-for:0801 schema:inDefinedTermSet anzsrc-for:
98 schema:name Artificial Intelligence and Image Processing
99 rdf:type schema:DefinedTerm
100 sg:person.011410250615.43 schema:affiliation grid-institutes:grid.10267.32
101 schema:familyName Šafránek
102 schema:givenName David
103 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011410250615.43
104 rdf:type schema:Person
105 sg:person.012266350607.01 schema:affiliation grid-institutes:grid.10267.32
106 schema:familyName Mertová
107 schema:givenName Lukrécia
108 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012266350607.01
109 rdf:type schema:Person
110 sg:person.013614147255.44 schema:affiliation grid-institutes:grid.10267.32
111 schema:familyName Troják
112 schema:givenName Matej
113 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013614147255.44
114 rdf:type schema:Person
115 sg:person.0645117057.83 schema:affiliation grid-institutes:grid.10267.32
116 schema:familyName Brim
117 schema:givenName Luboš
118 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0645117057.83
119 rdf:type schema:Person
120 grid-institutes:grid.10267.32 schema:alternateName Systems Biology Laboratory, Masaryk University, Brno, Czech Republic
121 schema:name Systems Biology Laboratory, Masaryk University, Brno, Czech Republic
122 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...