Understanding Evolutionary Potential in Virtual CPU Instruction Set Architectures
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Mendeley | Further Information

{"title"=>"Understanding evolutionary potential in virtual CPU instruction set architectures", "type"=>"journal", "authors"=>[{"first_name"=>"David M.", "last_name"=>"Bryson", "scopus_author_id"=>"55617532300"}, {"first_name"=>"Charles", "last_name"=>"Ofria", "scopus_author_id"=>"8110205600"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"doi"=>"10.1371/journal.pone.0083242", "scopus"=>"2-s2.0-84893453066", "issn"=>"19326203", "pui"=>"372292883", "pmid"=>"24376669", "sgr"=>"84893453066"}, "id"=>"f5884af9-bf1b-3b04-b121-fc5ccdb4c5c0", "abstract"=>"We investigate fundamental decisions in the design of instruction set architectures for linear genetic programs that are used as both model systems in evolutionary biology and underlying solution representations in evolutionary computation. We subjected digital organisms with each tested architecture to seven different computational environments designed to present a range of evolutionary challenges. Our goal was to engineer a general purpose architecture that would be effective under a broad range of evolutionary conditions. We evaluated six different types of architectural features for the virtual CPUs: (1) genetic flexibility: we allowed digital organisms to more precisely modify the function of genetic instructions, (2) memory: we provided an increased number of registers in the virtual CPUs, (3) decoupled sensors and actuators: we separated input and output operations to enable greater control over data flow. We also tested a variety of methods to regulate expression: (4) explicit labels that allow programs to dynamically refer to specific genome positions, (5) position-relative search instructions, and (6) multiple new flow control instructions, including conditionals and jumps. Each of these features also adds complication to the instruction set and risks slowing evolution due to epistatic interactions. Two features (multiple argument specification and separated I/O) demonstrated substantial improvements in the majority of test environments, along with versions of each of the remaining architecture modifications that show significant improvements in multiple environments. However, some tested modifications were detrimental, though most exhibit no systematic effects on evolutionary potential, highlighting the robustness of digital evolution. Combined, these observations enhance our understanding of how instruction architecture impacts evolutionary potential, enabling the creation of architectures that support more rapid evolution of complex solutions to a broad range of challenges.", "link"=>"http://www.mendeley.com/research/understanding-evolutionary-potential-virtual-cpu-instruction-set-architectures", "reader_count"=>10, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>1, "Student > Ph. D. Student"=>3, "Other"=>2, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>1, "Student > Ph. D. Student"=>3, "Other"=>2, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>4, "Medicine and Dentistry"=>1, "Design"=>1, "Computer Science"=>3}, "reader_count_by_subdiscipline"=>{"Design"=>{"Design"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}}, "reader_count_by_country"=>{"Spain"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1327719"], "description"=>"<p>Task success results of the LABEL-SEQ-DIRECT and SPLIT-IO instruction set architectures. Each entry shows the median normalized task success in the respective environment, with confidence intervals in parentheses. Bold entries denote significant (, Wilcoxon rank-sum test) deviations.</p>", "links"=>[], "tags"=>[], "article_id"=>886029, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.t011", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SPLIT_IO_Architecture_Task_Success_/886029", "title"=>"SPLIT-IO Architecture Task Success.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327718"], "description"=>"<p>Fitness results of the LABEL-SEQ-DIRECT and SPLIT-IO instruction set architectures. Each entry shows the median log population mean fitness in the respective environment, with confidence intervals in parentheses. Bold entries indicate significant (, Wilcoxon rank-sum test) deviations after sequential Bonferroni correction.</p>", "links"=>[], "tags"=>["split-io"], "article_id"=>886028, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.t010", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_bf_SPLIT_IO_Architecture_Fitness_/886028", "title"=>"bf SPLIT-IO Architecture Fitness.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327715"], "description"=>"<p>Instruction set by row, with marks in each column indicating that the set contains the relevant instruction group.</p>", "links"=>[], "tags"=>["sets"], "article_id"=>886025, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.t003", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_FLOW_Instruction_Sets_Tested_/886025", "title"=>"FLOW Instruction Sets Tested.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327713"], "description"=>"<p>Task success results of the HEADS and FULLY-ASSOCIATIVE (FA) instruction set architectures. Each entry shows the median normalized task success in the respective environment, with confidence intervals in parentheses. Bold entries denote significant (, Wilcoxon rank-sum test) deviations.</p>", "links"=>[], "tags"=>["fully-associative", "architectures"], "article_id"=>886023, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.t005", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_HEADS_and_FULLY_ASSOCIATIVE_Architectures_Task_Success_/886023", "title"=>"HEADS and FULLY-ASSOCIATIVE Architectures Task Success.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327714"], "description"=>"<p>Fitness results of the HEADS and FULLY-ASSOCIATIVE (FA) instruction set architectures, where multiple nop arguments can modify the behavior of an instruction. Each entry shows the median log population mean fitness in the respective environment, with confidence intervals in parentheses. Bold entries indicate significant (, Wilcoxon rank-sum test) deviations after sequential Bonferroni correction.</p>", "links"=>[], "tags"=>["fully-associative", "architectures"], "article_id"=>886024, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.t004", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_HEADS_and_FULLY_ASSOCIATIVE_Architectures_Fitness_/886024", "title"=>"HEADS and FULLY-ASSOCIATIVE Architectures Fitness.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327727"], "description"=>"<p>Task success results for the base HEADS and the HEADS-EX instruction set architectures. The HEADS-EX architecture includes features from all six tested feature groups, including fully associative arguments, six registers, direct-matched labels, split-I/O, directional search instructions, the ifx instruction, and conditional mov-head instructions. Each entry shows the median normalized task success in the respective environment, with confidence intervals in parentheses. Bold entries denote significant (, Wilcoxon rank-sum test) deviations.</p>", "links"=>[], "tags"=>["heads-ex", "architectures"], "article_id"=>886037, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.t017", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_HEADS_and_HEADS_EX_Architectures_Task_Success_/886037", "title"=>"HEADS and HEADS-EX Architectures Task Success.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327712"], "description"=>"<p>Fitness results of the Register -series instruction set architectures, which vary the number of registers available in the virtual CPUs. Each entry shows the median log population mean fitness in the respective environment, with confidence intervals in parentheses. Bold entries indicate significant (, Wilcoxon rank-sum test) deviations after sequential Bonferroni correction.</p>", "links"=>[], "tags"=>["architectures"], "article_id"=>886022, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.t006", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_REGISTER_Series_Architectures_Fitness_/886022", "title"=>"REGISTER Series Architectures Fitness.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327709"], "description"=>"<p>Normalized task success distributions of selected Flow -series instruction sets in the Sort-10 environment.</p>", "links"=>[], "tags"=>["distributions", "-series", "sets", "sort-10"], "article_id"=>886019, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.g002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Normalized_task_success_distributions_of_selected_Flow_series_instruction_sets_in_the_Sort_10_environment_/886019", "title"=>"Normalized task success distributions of selected Flow -series instruction sets in the Sort-10 environment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327726"], "description"=>"<p>Fitness results for the base HEADS and the HEADS-EX instruction set architectures. The HEADS-EX architecture includes features from all six tested feature groups, including fully associative arguments, six registers, direct-matched labels, split-I/O, directional search instructions, the ifx instruction, and conditional mov-head instructions. Each entry shows the median log population mean fitness in the respective environment, with confidence intervals in parentheses. Bold entries indicate significant (, Wilcoxon rank-sum test) deviations.</p>", "links"=>[], "tags"=>["heads-ex", "architectures"], "article_id"=>886036, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.t016", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_HEADS_and_HEADS_EX_Architectures_Fitness_/886036", "title"=>"HEADS and HEADS-EX Architectures Fitness.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327723"], "description"=>"<p>Task success results of the FLOW-series instruction set architectures. Each entry shows the median normalized task success in the respective environment, with confidence intervals in parentheses. Bold entries denote significant (, Wilcoxon rank-sum test) deviations.</p>", "links"=>[], "tags"=>["architectures"], "article_id"=>886033, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.t015", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_FLOW_Series_Architectures_Task_Success_/886033", "title"=>"FLOW Series Architectures Task Success.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327708"], "description"=>"<p>Registers (upper right), stacks (lower right), genomic program (left), heads (middle), and environmental channels (lower right). The solid lines depict the default Heads architectural features. The dashed lines show some of the modifications tested.</p>", "links"=>[], "tags"=>["Avida"], "article_id"=>886018, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.g001", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_architecture_of_the_Avida_virtual_CPU_/886018", "title"=>"The architecture of the Avida virtual CPU.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327721"], "description"=>"<p>Task success results of the SEARCH-series instruction set architectures. Each entry shows the median normalized task success in the respective environment, with confidence intervals in parentheses. Bold entries denote significant (, Wilcoxon rank-sum test) deviations.</p>", "links"=>[], "tags"=>["architectures"], "article_id"=>886031, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.t013", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SEARCH_Series_Architectures_Task_Success_/886031", "title"=>"SEARCH Series Architectures Task Success.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327722"], "description"=>"<p>Fitness results of the FLOW-series instruction set architectures. Each entry shows the median log population mean fitness in the respective environment, with confidence intervals in parentheses. Bold entries indicate significant (, Wilcoxon rank-sum test) deviations after sequential Bonferroni correction.</p>", "links"=>[], "tags"=>["architectures"], "article_id"=>886032, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.t014", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_FLOW_Series_Architectures_Fitness_/886032", "title"=>"FLOW Series Architectures Fitness.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327720"], "description"=>"<p>Fitness results of the SEARCH-series instruction set architectures. Each entry shows the median log population mean fitness in the respective environment, with confidence intervals in parentheses. Bold entries indicate significant (, Wilcoxon rank-sum test) deviations after sequential Bonferroni correction.</p>", "links"=>[], "tags"=>["architectures"], "article_id"=>886030, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.t012", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SEARCH_Series_Architectures_Fitness_/886030", "title"=>"SEARCH Series Architectures Fitness.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327717"], "description"=>"<p>Description of the instructions used across all tested instruction set architectures. A register name (AX, BX, CX, etc.) or head (IP, FLOW, etc.) surrounded by question marks refers to the default argument used when executed, subject to nop modi_cation. Instructions depicted in <b>bold</b> are in the default Heads instruction set.</p>", "links"=>[], "tags"=>[], "article_id"=>886027, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.t001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Instruction_Glossary_/886027", "title"=>"Instruction Glossary.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327716"], "description"=>"<p>Marks in each column indicating that the set contains the relevant instruction.</p>", "links"=>[], "tags"=>["sets"], "article_id"=>886026, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.t002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_LABEL_Instruction_Sets_Tested_/886026", "title"=>"LABEL Instruction Sets Tested.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327711"], "description"=>"<p>Task success results of the REGISTER-series instruction set architectures. Each entry shows the median normalized task success in the respective environment, with confidence intervals in parentheses. Bold entries denote significant (, Wilcoxon rank-sum test) deviations.</p>", "links"=>[], "tags"=>["architectures"], "article_id"=>886021, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.t007", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_REGISTER_Series_Architectures_Task_Success_/886021", "title"=>"REGISTER Series Architectures Task Success.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327725"], "description"=>"<p>Fitness results of the LABEL-series instruction set architectures. Each entry shows the median log population mean fitness in the respective environment, with confidence intervals in parentheses. Bold entries indicate significant (, Wilcoxon rank-sum test) deviations after sequential Bonferroni correction.</p>", "links"=>[], "tags"=>["architectures"], "article_id"=>886035, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.t008", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_LABEL_Series_Architectures_Fitness_/886035", "title"=>"LABEL Series Architectures Fitness.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327710"], "description"=>"<p>The evolutionary potential of the architecture selected as the basis for further experiments in each series (shown in bold) is displayed (right) for the Logic-9, Logic-77, Match-12, Fibonacci-32, Sort-10, Limited-9, and Navigation environments, respectively. Up arrows (black) indicate increased potential, down arrows (gray) indicate decreased potential, and double ended arrows (white) denote no significant trend. In general, FA (fully-associative) and Split-IO (separated input and output operations) demonstrated broadly beneficial impacts on evolutionary potential. The remaining tested modifications highlight the robustness of digital evolution, exhibiting no systematic effects on evolutionary potential.</p>", "links"=>[], "tags"=>["tested", "modifications"], "article_id"=>886020, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.g003", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_order_and_relationship_of_all_tested_architecture_modifications_center_organized_by_instruction_set_series_left_/886020", "title"=>"The order and relationship of all tested architecture modifications (center), organized by instruction set series (left).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-23 04:21:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/1327724"], "description"=>"<p>Task success results of the LABEL-series instruction set architectures. Each entry shows the median normalized task success in the respective environment, with confidence intervals in parentheses. Bold entries denote significant (, Wilcoxon rank-sum test) deviations.</p>", "links"=>[], "tags"=>["architectures"], "article_id"=>886034, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["David M. Bryson", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0083242.t009", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_LABEL_Series_Architectures_Task_Success_/886034", "title"=>"LABEL Series Architectures Task Success.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-23 04:21:35"}

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