Duration of Response

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

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

1# Reference solution for the yamaa benchmark adam-adtte-dor (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(RESPDT = col_date(), NACTDT = col_date(), .default = col_character())13)14adrs <- read_csv(15  "/app/input/adrs_raw.csv",16  col_types = cols(ASEQ = col_integer(), ADT = col_date(), .default = col_character())17)18ds <- read_csv(19  "/app/input/ds.csv",20  col_types = cols(DSSEQ = col_integer(), DSSTDTC = col_date(), .default = col_character())21)2223# Earliest progression and death, lowest sequence number on a tie.24progression <- adrs |>25  filter(AVALC %in% "PD", !is.na(ADT)) |>26  arrange(USUBJID, ADT, ASEQ) |>27  distinct(USUBJID, .keep_all = TRUE) |>28  select(USUBJID, PDDT = ADT, PDSEQ = ASEQ)2930death <- ds |>31  filter(DSDECOD %in% "DEATH", !is.na(DSSTDTC)) |>32  arrange(USUBJID, DSSTDTC, DSSEQ) |>33  distinct(USUBJID, .keep_all = TRUE) |>34  select(USUBJID, DTHDT = DSSTDTC, DTHSEQ = DSSEQ)3536# Last evaluable assessment (a date and a response other than NE), highest37# sequence number on a tie.38last_assessment <- adrs |>39  filter(!is.na(ADT), !is.na(AVALC), AVALC != "NE") |>40  arrange(USUBJID, desc(ADT), desc(ASEQ)) |>41  distinct(USUBJID, .keep_all = TRUE) |>42  select(USUBJID, LASTDT = ADT, LASTSEQ = ASEQ)4344# Where ADT comes from, for each outcome.45sources <- tribble(46  ~OUTCOME,                           ~SRCDOM, ~SRCVAR,47  "DISEASE PROGRESSION",              "ADRS",  "ADT",48  "DEATH",                            "DS",    "DSSTDTC",49  "LAST TUMOUR ASSESSMENT",           "ADRS",  "ADT",50  "START OF NEW ANTI-CANCER THERAPY", "ADSL",  "NACTDT"51)5253adtte <- adsl |>54  filter(!is.na(RESPDT)) |>55  left_join(progression, by = "USUBJID") |>56  left_join(death, by = "USUBJID") |>57  left_join(last_assessment, by = "USUBJID") |>58  mutate(59    # The first event; progression wins a same-day tie with death.60    EVENT = case_when(61      !is.na(PDDT) & (is.na(DTHDT) | PDDT <= DTHDT) ~ "DISEASE PROGRESSION",62      !is.na(DTHDT) ~ "DEATH"63    ),64    EVENTDT = if_else(EVENT == "DEATH", DTHDT, PDDT),65    # An event after the start of new therapy does not count.66    EVENT = if_else(!is.na(NACTDT) & EVENTDT > NACTDT, NA_character_, EVENT),67    # Without a counted event, the record is censored at the earlier of the68    # last evaluable assessment and the start of new therapy.69    OUTCOME = case_when(70      !is.na(EVENT) ~ EVENT,71      !is.na(LASTDT) & (is.na(NACTDT) | LASTDT <= NACTDT) ~ "LAST TUMOUR ASSESSMENT",72      !is.na(NACTDT) ~ "START OF NEW ANTI-CANCER THERAPY"73    ),74    ADT = case_when(75      OUTCOME == "DISEASE PROGRESSION" ~ PDDT,76      OUTCOME == "DEATH" ~ DTHDT,77      OUTCOME == "LAST TUMOUR ASSESSMENT" ~ LASTDT,78      OUTCOME == "START OF NEW ANTI-CANCER THERAPY" ~ NACTDT79    ),80    SRCSEQ = case_when(81      OUTCOME == "DISEASE PROGRESSION" ~ PDSEQ,82      OUTCOME == "DEATH" ~ DTHSEQ,83      OUTCOME == "LAST TUMOUR ASSESSMENT" ~ LASTSEQ84    ),85    PARAMCD = "DOR",86    PARAM = "Duration of Response",87    STARTDT = RESPDT,88    AVAL = as.integer(ADT - STARTDT) + 1L,89    CNSR = if_else(is.na(EVENT), 1L, 0L),90    EVNTDESC = coalesce(EVENT, "CENSORED"),91    CNSDTDSC = if_else(is.na(EVENT), OUTCOME, NA_character_)92  ) |>93  left_join(sources, by = "OUTCOME") |>94  select(95    STUDYID, USUBJID, PARAMCD, PARAM, STARTDT, ADT, AVAL, CNSR, EVNTDESC,96    CNSDTDSC, SRCDOM, SRCVAR, SRCSEQ97  )9899dir.create("/app/output", showWarnings = FALSE)100write_csv(adtte, "/app/output/adtte.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adtte-dor (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"""Create an ADTTE dataset (Duration of Response) from ADRS_RAW, ADSL and DS.89One record per subject whose ADSL RESPDT is not blank.10"""1112import csv13from datetime import date1415INPUT_DIR = "/app/input"16OUTPUT_DIR = "/app/output"171819def parse_date(text):20    text = (text or "").strip()21    if not text:22        return None23    return date.fromisoformat(text)242526def read_csv(name):27    with open(f"{INPUT_DIR}/{name}", newline="") as handle:28        return list(csv.DictReader(handle))293031def main():32    adsl = read_csv("adsl.csv")33    adrs = read_csv("adrs_raw.csv")34    ds = read_csv("ds.csv")3536    adrs_by_subject = {}37    for row in adrs:38        adrs_by_subject.setdefault(row["USUBJID"], []).append(row)3940    ds_by_subject = {}41    for row in ds:42        ds_by_subject.setdefault(row["USUBJID"], []).append(row)4344    out_rows = []45    for subj in adsl:46        respdt = parse_date(subj["RESPDT"])47        if respdt is None:48            continue49        usubjid = subj["USUBJID"]50        therapy_start = parse_date(subj["NACTDT"])5152        assessments = adrs_by_subject.get(usubjid, [])5354        # Progression: earliest dated assessment with response "PD";55        # ties on that date go to the lowest ASEQ.56        pd_records = [57            r for r in assessments58            if r["AVALC"].strip() == "PD" and parse_date(r["ADT"]) is not None59        ]60        prog_date = None61        prog_seq = None62        if pd_records:63            prog_date = min(parse_date(r["ADT"]) for r in pd_records)64            prog_seq = min(65                int(r["ASEQ"]) for r in pd_records66                if parse_date(r["ADT"]) == prog_date67            )6869        # Death: earliest DS record with a "DEATH" term.70        death_records = [71            r for r in ds_by_subject.get(usubjid, [])72            if r["DSDECOD"].strip() == "DEATH" and parse_date(r["DSSTDTC"]) is not None73        ]74        death_date = None75        death_seq = None76        if death_records:77            death_date = min(parse_date(r["DSSTDTC"]) for r in death_records)78            death_seq = min(79                int(r["DSSEQ"]) for r in death_records80                if parse_date(r["DSSTDTC"]) == death_date81            )8283        # Event date: earlier of progression and death.84        event_date = None85        event_kind = None86        if prog_date is not None and (death_date is None or prog_date <= death_date):87            event_date, event_kind = prog_date, "PD"88        elif death_date is not None:89            event_date, event_kind = death_date, "DEATH"9091        # The event counts only when it does not fall after the therapy92        # start date; an event on the therapy start date itself counts.93        counted = event_date is not None and (94            therapy_start is None or event_date <= therapy_start95        )9697        # Last valid tumour assessment: latest dated assessment whose98        # response is not "NE"; ties on that date go to the highest ASEQ.99        valid_records = [100            r for r in assessments101            if r["AVALC"].strip() != "NE" and parse_date(r["ADT"]) is not None102        ]103        last_valid_date = None104        last_valid_seq = None105        if valid_records:106            last_valid_date = max(parse_date(r["ADT"]) for r in valid_records)107            last_valid_seq = max(108                int(r["ASEQ"]) for r in valid_records109                if parse_date(r["ADT"]) == last_valid_date110            )111112        if counted:113            adt = event_date114            cnsr = 0115            if event_kind == "PD":116                evntdesc = "DISEASE PROGRESSION"117                cnsdtdsc = ""118                srcdom = "ADRS"119                srcvar = "ADT"120                srcseq = prog_seq121            else:122                evntdesc = "DEATH"123                cnsdtdsc = ""124                srcdom = "DS"125                srcvar = "DSSTDTC"126                srcseq = death_seq127        else:128            cnsr = 1129            evntdesc = "CENSORED"130            candidates = [131                d for d in (last_valid_date, therapy_start) if d is not None132            ]133            adt = min(candidates) if candidates else None134            if adt is not None and adt == last_valid_date:135                cnsdtdsc = "LAST TUMOUR ASSESSMENT"136                srcdom = "ADRS"137                srcvar = "ADT"138                srcseq = last_valid_seq139            else:140                cnsdtdsc = "START OF NEW ANTI-CANCER THERAPY"141                srcdom = "ADSL"142                srcvar = "NACTDT"143                srcseq = None144145        aval = ""146        if adt is not None:147            aval = max(1, (adt - respdt).days + 1)148149        out_rows.append({150            "STUDYID": subj["STUDYID"],151            "USUBJID": usubjid,152            "PARAMCD": "DOR",153            "PARAM": "Duration of Response",154            "STARTDT": respdt.isoformat(),155            "ADT": adt.isoformat() if adt is not None else "",156            "AVAL": aval,157            "CNSR": cnsr,158            "EVNTDESC": evntdesc,159            "CNSDTDSC": cnsdtdsc,160            "SRCDOM": srcdom,161            "SRCVAR": srcvar,162            "SRCSEQ": srcseq if srcseq is not None else "",163        })164165    columns = [166        "STUDYID", "USUBJID", "PARAMCD", "PARAM", "STARTDT", "ADT", "AVAL",167        "CNSR", "EVNTDESC", "CNSDTDSC", "SRCDOM", "SRCVAR", "SRCSEQ",168    ]169    with open(f"{OUTPUT_DIR}/adtte.csv", "w", newline="") as handle:170        writer = csv.DictWriter(handle, fieldnames=columns)171        writer.writeheader()172        writer.writerows(out_rows)173174175if __name__ == "__main__":176    main()

1/* opensas reference solution for the yamaa benchmark adam-adtte-dor.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data adrs_raw;6  length STUDYID USUBJID ADT AVALC $1024;7  infile "/app/input/adrs_raw.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. ASEQ ADT : $char1024. AVALC : $char1024.;9run;1011data adsl;12  length STUDYID USUBJID RESPDT NACTDT $1024;13  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. RESPDT : $char1024. NACTDT : $char1024.;15run;1617data ds;18  length STUDYID USUBJID DSDECOD DSSTDTC $1024;19  infile "/app/input/ds.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;20  input STUDYID : $char1024. USUBJID : $char1024. DSSEQ DSDECOD : $char1024. DSSTDTC : $char1024.;21run;2223proc sql;24  create table usable as select a.* from adrs_raw as a inner join adsl as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID where a.ADT ne '' and a.AVALC ne 'NE';25  create table progression as select a.* from adrs_raw as a inner join adsl as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID where a.ADT ne '' and a.AVALC='PD' and a.AVALC ne 'NE' and (missing(b.NACTDT) or a.ADT<=b.NACTDT);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.DSSTDTC ne '' and (missing(b.NACTDT) or a.DSSTDTC<=b.NACTDT);27quit;28proc sort data=progression; by STUDYID USUBJID ADT ASEQ; run;29data pd; set progression; by STUDYID USUBJID; if first.USUBJID; keep STUDYID USUBJID ADT ASEQ; rename ADT=PDDT ASEQ=PDSEQ; run;30proc sort data=deaths; by STUDYID USUBJID DSSTDTC DSSEQ; run;31data death; set deaths; by STUDYID USUBJID; if first.USUBJID; keep STUDYID USUBJID DSSTDTC DSSEQ; rename DSSTDTC=DEATHDT DSSEQ=DEATHSEQ; run;32proc sort data=usable; by STUDYID USUBJID descending ADT descending ASEQ; run;33data lastassessment; set usable; by STUDYID USUBJID; if first.USUBJID; keep STUDYID USUBJID ADT ASEQ; rename ADT=LASTDT ASEQ=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; if not missing(RESPDT);39  PARAMCD='DOR'; PARAM='Duration of Response'; STARTDT=RESPDT;40  if not missing(PDDT) and (missing(DEATHDT) or PDDT<=DEATHDT) then do; ADT=PDDT; CNSR=0; EVNTDESC='DISEASE PROGRESSION'; SRCDOM='ADRS'; SRCVAR='ADT'; SRCSEQ=PDSEQ; end;41  else if not missing(DEATHDT) then do; ADT=DEATHDT; CNSR=0; EVNTDESC='DEATH'; SRCDOM='DS'; SRCVAR='DSSTDTC'; SRCSEQ=DEATHSEQ; end;42  else do;43    CNSR=1; EVNTDESC='CENSORED';44    if not missing(NACTDT) and (missing(LASTDT) or NACTDT<LASTDT) then do; ADT=NACTDT; CNSDTDSC='START OF NEW ANTI-CANCER THERAPY'; SRCDOM='ADSL'; SRCVAR='NACTDT'; end;45    else do; ADT=LASTDT; CNSDTDSC='LAST TUMOUR ASSESSMENT'; SRCDOM='ADRS'; SRCVAR='ADT'; SRCSEQ=LASTSEQ; end;46  end;47  if not missing(ADT) and not missing(STARTDT) then AVAL=input(ADT,yymmdd10.)-input(STARTDT,yymmdd10.)+1;48run;4950proc sql;51  create table final as select STUDYID, USUBJID, PARAMCD, PARAM, STARTDT, ADT, AVAL, CNSR, EVNTDESC, CNSDTDSC, SRCDOM, SRCVAR, SRCSEQ from result;52quit;53proc export data=final outfile="/app/output/adtte.csv" dbms=csv replace; run;