{"id":"https://openalex.org/W4384833498","doi":"https://doi.org/10.1145/3597031.3597050","title":"Mutation Tree Reconstruction of Tumor Cells on FPGAs Using a Bit-Level Matrix Representation","display_name":"Mutation Tree Reconstruction of Tumor Cells on FPGAs Using a Bit-Level Matrix Representation","publication_year":2023,"publication_date":"2023-06-14","ids":{"openalex":"https://openalex.org/W4384833498","doi":"https://doi.org/10.1145/3597031.3597050"},"language":"en","primary_location":{"id":"doi:10.1145/3597031.3597050","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3597031.3597050","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3597031.3597050","source":null,"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 13th International Symposium on Highly Efficient Accelerators and Reconfigurable Technologies","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3597031.3597050","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091933606","display_name":"Jan-Oliver Opdenh\u00f6vel","orcid":"https://orcid.org/0000-0003-2314-2784"},"institutions":[{"id":"https://openalex.org/I206945453","display_name":"Paderborn University","ror":"https://ror.org/058kzsd48","country_code":"DE","type":"education","lineage":["https://openalex.org/I206945453"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jan-Oliver Opdenh\u00f6vel","raw_affiliation_strings":["Paderborn Center for Parallel Computing, Paderborn University, Germany"],"raw_orcid":"https://orcid.org/0000-0003-2314-2784","affiliations":[{"raw_affiliation_string":"Paderborn Center for Parallel Computing, Paderborn University, Germany","institution_ids":["https://openalex.org/I206945453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039484700","display_name":"Christian Plessl","orcid":"https://orcid.org/0000-0001-5728-9982"},"institutions":[{"id":"https://openalex.org/I206945453","display_name":"Paderborn University","ror":"https://ror.org/058kzsd48","country_code":"DE","type":"education","lineage":["https://openalex.org/I206945453"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Christian Plessl","raw_affiliation_strings":["Paderborn Center for Parallel Computing, Paderborn University, Germany"],"raw_orcid":"https://orcid.org/0000-0001-5728-9982","affiliations":[{"raw_affiliation_string":"Paderborn Center for Parallel Computing, Paderborn University, Germany","institution_ids":["https://openalex.org/I206945453"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009852288","display_name":"Tobias Kenter","orcid":"https://orcid.org/0000-0002-5088-0267"},"institutions":[{"id":"https://openalex.org/I206945453","display_name":"Paderborn University","ror":"https://ror.org/058kzsd48","country_code":"DE","type":"education","lineage":["https://openalex.org/I206945453"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tobias Kenter","raw_affiliation_strings":["Paderborn Center for Parallel Computing, Paderborn University, Germany"],"raw_orcid":"https://orcid.org/0000-0002-5088-0267","affiliations":[{"raw_affiliation_string":"Paderborn Center for Parallel Computing, Paderborn University, Germany","institution_ids":["https://openalex.org/I206945453"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I206945453"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"27","last_page":"34"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11321","display_name":"Error Correcting Code Techniques","score":0.995199978351593,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.9919999837875366,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7394986748695374},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5318531394004822},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.5188154578208923},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.47650232911109924},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4750754237174988},{"id":"https://openalex.org/keywords/monte-carlo-tree-search","display_name":"Monte Carlo tree search","score":0.45963793992996216},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4563274383544922},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.42564883828163147},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.4216915965080261},{"id":"https://openalex.org/keywords/latency","display_name":"Latency (audio)","score":0.4184780418872833},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.415014386177063},{"id":"https://openalex.org/keywords/monte-carlo-method","display_name":"Monte Carlo method","score":0.30968427658081055},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18193799257278442},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1602950394153595},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.1601749062538147},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.14189013838768005},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10240817070007324}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7394986748695374},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5318531394004822},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.5188154578208923},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.47650232911109924},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4750754237174988},{"id":"https://openalex.org/C46149586","wikidata":"https://www.wikidata.org/wiki/Q11785332","display_name":"Monte Carlo tree search","level":3,"score":0.45963793992996216},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4563274383544922},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.42564883828163147},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.4216915965080261},{"id":"https://openalex.org/C82876162","wikidata":"https://www.wikidata.org/wiki/Q17096504","display_name":"Latency (audio)","level":2,"score":0.4184780418872833},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.415014386177063},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.30968427658081055},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18193799257278442},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1602950394153595},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.1601749062538147},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.14189013838768005},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10240817070007324},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3597031.3597050","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3597031.3597050","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3597031.3597050","source":null,"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 13th International Symposium on Highly Efficient Accelerators and Reconfigurable Technologies","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3597031.3597050","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3597031.3597050","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3597031.3597050","source":null,"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 13th International Symposium on Highly Efficient Accelerators and Reconfigurable Technologies","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4384833498.pdf","grobid_xml":"https://content.openalex.org/works/W4384833498.grobid-xml"},"referenced_works_count":5,"referenced_works":["https://openalex.org/W1566539040","https://openalex.org/W1978885894","https://openalex.org/W1992519395","https://openalex.org/W2762185802","https://openalex.org/W2950629094"],"related_works":["https://openalex.org/W2571592646","https://openalex.org/W4247855592","https://openalex.org/W2567165815","https://openalex.org/W2111241003","https://openalex.org/W2740304877","https://openalex.org/W4200391368","https://openalex.org/W3008625068","https://openalex.org/W3128807919","https://openalex.org/W3176411177","https://openalex.org/W3035501883"],"abstract_inverted_index":{"Reconstructing":[0],"the":[1,9,105],"mutation":[2],"history":[3],"of":[4,11,34],"a":[5,12,21,25,41,57,86],"cancer":[6],"cell":[7],"in":[8,98],"form":[10],"phylogenetic":[13],"tree":[14],"from":[15],"noisy":[16],"genome":[17],"sequencing":[18],"data":[19],"requires":[20],"likelihood":[22],"model":[23],"and":[24,50,93,102],"search":[26,42],"or":[27],"optimization":[28],"strategy.":[29],"The":[30,89],"\u201cSingle":[31],"Cell":[32],"Inference":[33],"Tumor":[35],"Evolution\u201d":[36],"(SCITE)":[37],"software":[38,108],"performs":[39],"such":[40],"via":[43],"Monte":[44],"Carlo":[45],"Markov":[46],"Chains":[47],"that":[48,75],"explore":[49],"evaluate":[51],"different":[52],"random":[53],"update":[54],"operations":[55,79],"on":[56,85],"current":[58],"candidate":[59],"tree.":[60],"In":[61],"this":[62],"work,":[63],"we":[64],"present":[65],"an":[66],"FPGA":[67],"accelerator":[68],"design":[69,91],"(denoted":[70],"as":[71,83],"\u201cbit-based":[72],"SCITE\u201d":[73],"(bbSCITE))":[74],"implements":[76],"all":[77],"required":[78],"with":[80],"deterministic":[81],"latency":[82],"bit-operations":[84],"matrix":[87],"representation.":[88],"largest":[90],"updates":[92],"counts":[94],"36100":[95],"set":[96],"bits":[97],"each":[99],"clock":[100],"cycle":[101],"thus":[103],"outperforms":[104],"original":[106],"single-threaded":[107],"reference":[109],"by":[110],"up":[111],"to":[112],"80":[113],"\u00d7.":[114]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}