Progression-Free Survival

1library(yamaa)23yamaa_spec("spec.yaml")$run()$output

1import yamaa23yamaa.spec("spec.yaml").run().output

1# Reference solution for the yamaa benchmark adam-adtte-pfs (R track).2#3# Written from the benchmark's full prompt and its inputs alone, as an agent4# would write it. Harbor's oracle agent runs it to check that the prompt can5# be solved and that the grader scores a correct answer 1.67library(dplyr, warn.conflicts = FALSE)8library(readr)910adsl <- read_csv(11  "/app/input/adsl.csv",12  col_types = cols(13    RANDDT = col_date(), NTXSTDT = col_date(), .default = col_character()14  )15)16rs <- read_csv(17  "/app/input/rs.csv",18  col_types = cols(RSSEQ = col_integer(), RSDTC = col_date(), .default = col_character())19)20ds <- read_csv(21  "/app/input/ds.csv",22  col_types = cols(DSSEQ = col_integer(), DSDTC = col_date(), .default = col_character())23)2425# The first adequate progression, the first death, and the last adequate26# assessment. Records sharing a date are ordered by sequence number.27progression <- rs |>28  filter(RSTESTCD %in% "OVRLRESP", RSSTRESC %in% "PD", ADEQFL %in% "Y", !is.na(RSDTC)) |>29  arrange(USUBJID, RSDTC, RSSEQ) |>30  distinct(USUBJID, .keep_all = TRUE) |>31  select(USUBJID, PDDT = RSDTC, PDSEQ = RSSEQ)3233death <- ds |>34  filter(DSDECOD %in% "DEATH", !is.na(DSDTC)) |>35  arrange(USUBJID, DSDTC, DSSEQ) |>36  distinct(USUBJID, .keep_all = TRUE) |>37  select(USUBJID, DTHDT = DSDTC, DTHSEQ = DSSEQ)3839last_assessment <- rs |>40  filter(RSTESTCD %in% "OVRLRESP", ADEQFL %in% "Y", !is.na(RSDTC)) |>41  arrange(USUBJID, desc(RSDTC), desc(RSSEQ)) |>42  distinct(USUBJID, .keep_all = TRUE) |>43  select(USUBJID, CENSORDT = RSDTC, LASTSEQ = RSSEQ)4445# The last adequate assessment dated on or before new-therapy start, for46# subjects who began one.47pre_therapy <- rs |>48  inner_join(select(adsl, USUBJID, NTXSTDT), by = "USUBJID") |>49  filter(50    RSTESTCD %in% "OVRLRESP", ADEQFL %in% "Y", !is.na(RSDTC),51    !is.na(NTXSTDT), RSDTC <= NTXSTDT52  ) |>53  arrange(USUBJID, desc(RSDTC), desc(RSSEQ)) |>54  distinct(USUBJID, .keep_all = TRUE) |>55  select(USUBJID, PRECENSORDT = RSDTC, PRESEQ = RSSEQ)5657adtte <- adsl |>58  left_join(progression, by = "USUBJID") |>59  left_join(death, by = "USUBJID") |>60  left_join(last_assessment, by = "USUBJID") |>61  left_join(pre_therapy, by = "USUBJID") |>62  mutate(63    PARAMCD = "PFS",64    PARAM = "Progression-Free Survival",65    STARTDT = RANDDT,66    # A progression or death dated after new-therapy start is not an event.67    PDDT = if_else(!is.na(NTXSTDT) & PDDT > NTXSTDT, as.Date(NA), PDDT),68    DTHDT = if_else(!is.na(NTXSTDT) & DTHDT > NTXSTDT, as.Date(NA), DTHDT),69    # The censoring assessment: the last adequate one overall, or the last70    # one dated on or before therapy start when therapy began.71    CENSORASSESSDT = if_else(is.na(NTXSTDT), CENSORDT, PRECENSORDT),72    CENSORSEQ = if_else(is.na(NTXSTDT), LASTSEQ, PRESEQ),73    # With no usable adequate assessment the subject is censored at74    # randomization, for a 1-day PFS.75    CENSORDT = coalesce(CENSORASSESSDT, STARTDT),76    EVENTDT = case_when(77      !is.na(PDDT) & !is.na(DTHDT) ~ pmin(PDDT, DTHDT),78      !is.na(PDDT) ~ PDDT,79      !is.na(DTHDT) ~ DTHDT80    ),81    # The event always wins, even after the last adequate assessment,82    # unless new anti-cancer therapy started first.83    CNSR = if_else(!is.na(EVENTDT), 0L, 1L),84    ADT = coalesce(EVENTDT, CENSORDT),85    AVAL = as.integer(ADT - STARTDT) + 1L,86    # A progression and a death on the same day count as progression.87    EVNTDESC = case_when(88      is.na(EVENTDT) ~ "CENSORED",89      !is.na(PDDT) & (is.na(DTHDT) | PDDT <= DTHDT) ~ "DISEASE PROGRESSION",90      .default = "DEATH"91    ),92    SRCDOM = case_when(93      EVNTDESC == "DEATH" ~ "DS",94      is.na(CENSORASSESSDT) ~ NA_character_,95      .default = "RS"96    ),97    SRCVAR = case_when(98      EVNTDESC == "DEATH" ~ "DSDTC",99      is.na(CENSORASSESSDT) ~ NA_character_,100      .default = "RSDTC"101    ),102    SRCSEQ = case_when(103      EVNTDESC == "DISEASE PROGRESSION" ~ PDSEQ,104      EVNTDESC == "DEATH" ~ DTHSEQ,105      is.na(CENSORASSESSDT) ~ NA_integer_,106      .default = CENSORSEQ107    )108  ) |>109  arrange(USUBJID) |>110  select(111    STUDYID, USUBJID, PARAMCD, PARAM, STARTDT, ADT, AVAL, CNSR, EVNTDESC,112    SRCDOM, SRCVAR, SRCSEQ113  )114115dir.create("/app/output", showWarnings = FALSE)116write_csv(adtte, "/app/output/adtte.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adtte-pfs (Python track).2#3# Written from the benchmark's full prompt and its inputs alone, as an agent4# would write it. Harbor's oracle agent runs it to check that the prompt can5# be solved and that the grader scores a correct answer 1.67"""Build ADTTE (PFS) from ADSL, DS, and RS per the task instruction.89Reads /app/input/{adsl,ds,rs}.csv and writes /app/output/adtte.csv with10one record per subject.11"""1213import csv14from datetime import date1516INPUT_DIR = "/app/input"17OUTPUT_PATH = "/app/output/adtte.csv"181920def parse_date(text):21    """Return a date for an ISO date string, or None when blank."""22    text = (text or "").strip()23    if not text:24        return None25    return date.fromisoformat(text)262728def read_rows(name):29    with open(f"{INPUT_DIR}/{name}", newline="", encoding="utf-8") as handle:30        return list(csv.DictReader(handle))313233def main():34    adsl = read_rows("adsl.csv")35    ds = read_rows("ds.csv")36    rs = read_rows("rs.csv")3738    # Per-subject new anti-cancer therapy start: only dates on or before39    # it are usable for events and censoring.40    ntx_by_subject = {}41    for subj in adsl:42        key = (subj["STUDYID"], subj["USUBJID"])43        ntx_by_subject[key] = parse_date(subj["NTXSTDT"])4445    def usable(key, day):46        ntx = ntx_by_subject.get(key)47        return ntx is None or day <= ntx4849    deaths = {}50    for row in ds:51        if row["DSDECOD"] != "DEATH":52            continue53        dthdt = parse_date(row["DSDTC"])54        if dthdt is None:55            continue56        key = (row["STUDYID"], row["USUBJID"])57        if not usable(key, dthdt):58            continue59        candidate = (dthdt, int(row["DSSEQ"]))60        if key not in deaths or candidate < deaths[key]:61            deaths[key] = candidate6263    progressions = {}64    last_adequate = {}65    for row in rs:66        if row["RSTESTCD"] != "OVRLRESP" or row["ADEQFL"] != "Y":67            continue68        adt = parse_date(row["RSDTC"])69        if adt is None:70            continue71        key = (row["STUDYID"], row["USUBJID"])72        if not usable(key, adt):73            continue74        seq = int(row["RSSEQ"])75        if row["RSSTRESC"] == "PD":76            candidate = (adt, seq)77            if key not in progressions or candidate < progressions[key]:78                progressions[key] = candidate79        latest = last_adequate.get(key)80        if latest is None or (adt, seq) > latest:81            last_adequate[key] = (adt, seq)8283    out_rows = []84    for subj in adsl:85        studyid = subj["STUDYID"]86        usubjid = subj["USUBJID"]87        key = (studyid, usubjid)88        startdt = parse_date(subj["RANDDT"])8990        prog = progressions.get(key)91        death = deaths.get(key)9293        srcdom = srcvar = srcseq = ""94        if prog is not None and (death is None or prog[0] <= death[0]):95            adt = prog[0]96            cnsr = 097            evntdesc = "DISEASE PROGRESSION"98            srcdom, srcvar, srcseq = "RS", "RSDTC", prog[1]99        elif death is not None:100            adt = death[0]101            cnsr = 0102            evntdesc = "DEATH"103            srcdom, srcvar, srcseq = "DS", "DSDTC", death[1]104        else:105            cnsr = 1106            evntdesc = "CENSORED"107            last = last_adequate.get(key)108            if last is None:109                # No usable adequate assessment: censored at randomization.110                adt = startdt111            else:112                adt = last[0]113                srcdom, srcvar, srcseq = "RS", "RSDTC", last[1]114115        aval = (adt - startdt).days + 1116117        out_rows.append(118            {119                "STUDYID": studyid,120                "USUBJID": usubjid,121                "PARAMCD": "PFS",122                "PARAM": "Progression-Free Survival",123                "STARTDT": startdt.isoformat(),124                "ADT": adt.isoformat(),125                "AVAL": aval,126                "CNSR": cnsr,127                "EVNTDESC": evntdesc,128                "SRCDOM": srcdom,129                "SRCVAR": srcvar,130                "SRCSEQ": srcseq,131            }132        )133134    fieldnames = [135        "STUDYID",136        "USUBJID",137        "PARAMCD",138        "PARAM",139        "STARTDT",140        "ADT",141        "AVAL",142        "CNSR",143        "EVNTDESC",144        "SRCDOM",145        "SRCVAR",146        "SRCSEQ",147    ]148    with open(OUTPUT_PATH, "w", newline="", encoding="utf-8") as handle:149        writer = csv.DictWriter(handle, fieldnames=fieldnames)150        writer.writeheader()151        writer.writerows(out_rows)152153154if __name__ == "__main__":155    main()

1/* opensas reference solution for the yamaa benchmark adam-adtte-pfs.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data adsl;6  length STUDYID USUBJID RANDDT NTXSTDT $1024;7  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. RANDDT : $char1024. NTXSTDT : $char1024.;9run;1011data ds;12  length STUDYID USUBJID DSDTC DSDECOD $1024;13  infile "/app/input/ds.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. DSSEQ DSDTC : $char1024. DSDECOD : $char1024.;15run;1617data rs;18  length STUDYID USUBJID RSTESTCD RSDTC RSSTRESC ADEQFL $1024;19  infile "/app/input/rs.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;20  input STUDYID : $char1024. USUBJID : $char1024. RSSEQ RSTESTCD : $char1024. RSDTC : $char1024. RSSTRESC : $char1024. ADEQFL : $char1024.;21run;2223proc sql;24  create table usable as select a.* from rs as a inner join adsl as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID where a.RSDTC ne '' and a.ADEQFL='Y' and a.RSTESTCD='OVRLRESP' and (missing(b.NTXSTDT) or a.RSDTC<=b.NTXSTDT);25  create table progression as select a.* from rs as a inner join adsl as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID where a.RSDTC ne '' and a.RSSTRESC='PD' and a.ADEQFL='Y' and a.RSTESTCD='OVRLRESP' and (missing(b.NTXSTDT) or a.RSDTC<=b.NTXSTDT);26  create table deaths as select a.* from ds as a inner join adsl as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID where a.DSDECOD='DEATH' and a.DSDTC ne '' and (missing(b.NTXSTDT) or a.DSDTC<=b.NTXSTDT);27quit;28proc sort data=progression; by STUDYID USUBJID RSDTC RSSEQ; run;29data pd; set progression; by STUDYID USUBJID; if first.USUBJID; keep STUDYID USUBJID RSDTC RSSEQ; rename RSDTC=PDDT RSSEQ=PDSEQ; run;30proc sort data=deaths; by STUDYID USUBJID DSDTC DSSEQ; run;31data death; set deaths; by STUDYID USUBJID; if first.USUBJID; keep STUDYID USUBJID DSDTC DSSEQ; rename DSDTC=DEATHDT DSSEQ=DEATHSEQ; run;32proc sort data=usable; by STUDYID USUBJID descending RSDTC descending RSSEQ; run;33data lastassessment; set usable; by STUDYID USUBJID; if first.USUBJID; keep STUDYID USUBJID RSDTC RSSEQ; rename RSDTC=LASTDT RSSEQ=LASTSEQ; run;34proc sql; create table joined as select a.*,b.PDDT,b.PDSEQ,c.DEATHDT,c.DEATHSEQ,d.LASTDT,d.LASTSEQ from adsl as a35  left join pd as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID left join death as c on a.STUDYID=c.STUDYID and a.USUBJID=c.USUBJID left join lastassessment as d on a.STUDYID=d.STUDYID and a.USUBJID=d.USUBJID; quit;36data result;37  length PARAMCD $8 PARAM $40 STARTDT ADT $10 EVNTDESC CNSDTDSC $40 SRCDOM $4 SRCVAR $16;38  set joined;39  PARAMCD='PFS'; PARAM='Progression-Free Survival'; STARTDT=RANDDT;40  if not missing(PDDT) and (missing(DEATHDT) or PDDT<=DEATHDT) then do; ADT=PDDT; CNSR=0; EVNTDESC='DISEASE PROGRESSION'; SRCDOM='RS'; SRCVAR='RSDTC'; SRCSEQ=PDSEQ; end;41  else if not missing(DEATHDT) then do; ADT=DEATHDT; CNSR=0; EVNTDESC='DEATH'; SRCDOM='DS'; SRCVAR='DSDTC'; SRCSEQ=DEATHSEQ; end;42  else do;43    CNSR=1; EVNTDESC='CENSORED';44    if not missing(LASTDT) then do; ADT=LASTDT; SRCDOM='RS'; SRCVAR='RSDTC'; SRCSEQ=LASTSEQ; end; else ADT=RANDDT;45  end;46  if not missing(ADT) and not missing(STARTDT) then AVAL=input(ADT,yymmdd10.)-input(STARTDT,yymmdd10.)+1;47run;4849proc sql;50  create table final as select STUDYID, USUBJID, PARAMCD, PARAM, STARTDT, ADT, AVAL, CNSR, EVNTDESC, SRCDOM, SRCVAR, SRCSEQ from result;51quit;52proc export data=final outfile="/app/output/adtte.csv" dbms=csv replace; run;