Time to Deterioration for a PRO Endpoint

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

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

1# Reference solution for the yamaa benchmark adam-adtte-pro-deterioration2# (R track).3#4# Written from the benchmark's full prompt and its inputs alone, as an agent5# would write it. Harbor's oracle agent runs it to check that the prompt can6# be solved and that the grader scores a correct answer 1.78library(dplyr, warn.conflicts = FALSE)9library(readr)10library(lubridate, warn.conflicts = FALSE)1112whole_months <- function(d1, d2) {13  m <- (year(d2) - year(d1)) * 12 + (month(d2) - month(d1))14  last <- days_in_month(d2)15  m - as.integer(day(d2) < day(d1) & day(d2) != last)16}1718adsl <- read_csv(19  "/app/input/adsl.csv",20  col_types = cols(21    RANDDT = col_date(), DTHDT = col_date(), .default = col_character()22  )23)24qs <- read_csv(25  "/app/input/qs.csv",26  col_types = cols(27    QSSEQ = col_integer(), ADT = col_date(), AVAL = col_integer(),28    .default = col_character()29  )30)31ds <- read_csv(32  "/app/input/ds.csv",33  col_types = cols(34    DSSEQ = col_integer(), DSDTC = col_date(), .default = col_character()35  )36)3738# Flag deteriorations as an internal step: the baseline is the earliest39# dated assessment with a score (a scoreless row cannot be the baseline:40# its null score would leave no later row able to meet the cutoff), and41# an assessment deteriorates when it is dated after the baseline and its42# score is at least 10 points below the baseline score.43baseline <- qs |>44  filter(!is.na(ADT), !is.na(AVAL)) |>45  arrange(STUDYID, USUBJID, ADT, QSSEQ) |>46  distinct(STUDYID, USUBJID, .keep_all = TRUE) |>47  select(STUDYID, USUBJID, BASEDT = ADT, BASEVAL = AVAL)4849qs_flagged <- qs |>50  left_join(baseline, by = c("STUDYID", "USUBJID")) |>51  mutate(52    DETERFL = if_else(53      !is.na(ADT) & !is.na(BASEDT) & ADT > BASEDT & !is.na(AVAL) &54        AVAL <= BASEVAL - 10L,55      "Y",56      NA_character_57    )58  ) |>59  select(STUDYID, USUBJID, QSSEQ, AVISIT, ADT, AVAL, DETERFL) |>60  arrange(USUBJID, QSSEQ)6162# The first deterioration per subject, earliest date then lowest sequence.63deter <- qs_flagged |>64  filter(DETERFL == "Y") |>65  arrange(STUDYID, USUBJID, ADT, QSSEQ) |>66  distinct(STUDYID, USUBJID, .keep_all = TRUE) |>67  select(STUDYID, USUBJID, DETERDT = ADT, DETERSEQ = QSSEQ)6869# The first censoring reason per subject. Only progression,70# discontinuation, and withdrawal count; any other DS record is ignored.71reason <- ds |>72  filter(73    DSDECOD %in% c(74      "DISEASE PROGRESSION", "STUDY DISCONTINUATION", "WITHDRAWAL OF CONSENT"75    )76  ) |>77  arrange(STUDYID, USUBJID, DSDTC, DSSEQ) |>78  distinct(STUDYID, USUBJID, .keep_all = TRUE) |>79  select(STUDYID, USUBJID, CENSORRSNDT = DSDTC, CENSORRSN = DSDECOD)8081# The latest assessment with a score dated on or before the censoring82# reason, with the latest sequence breaking a tied date; a scoreless row83# is not an evaluable assessment and cannot set the censoring date.84censor_qs <- qs_flagged |>85  inner_join(reason, by = c("STUDYID", "USUBJID")) |>86  filter(!is.na(ADT), !is.na(AVAL), ADT <= CENSORRSNDT) |>87  group_by(STUDYID, USUBJID) |>88  summarize(89    LASTQSLE = max(ADT),90    LASTQSSEQ = max(QSSEQ[ADT == max(ADT)]),91    .groups = "drop"92  )9394adtte <- adsl |>95  left_join(deter, by = c("STUDYID", "USUBJID")) |>96  left_join(reason, by = c("STUDYID", "USUBJID")) |>97  left_join(censor_qs, by = c("STUDYID", "USUBJID")) |>98  mutate(99    STARTDT = RANDDT,100    # Deterioration wins over death on the same date. Neither counts when101    # it falls after the first censoring reason: progression,102    # discontinuation, and withdrawal are censoring reasons, never events,103    # though a same-day deterioration or death still counts.104    DETER_EVENT = !is.na(DETERDT) & (is.na(DTHDT) | DETERDT <= DTHDT) &105      (is.na(CENSORRSNDT) | DETERDT <= CENSORRSNDT),106    DEATH_EVENT = !is.na(DTHDT) &107      (is.na(CENSORRSNDT) | DTHDT <= CENSORRSNDT),108    EVENTDT = case_when(109      DETER_EVENT ~ DETERDT,110      DEATH_EVENT ~ DTHDT,111      .default = as.Date(NA)112    ),113    CENSORDT = coalesce(LASTQSLE, STARTDT),114    ADT = coalesce(EVENTDT, CENSORDT),115    AVAL = whole_months(STARTDT, ADT),116    CNSR = if_else(!is.na(EVENTDT), 0L, 1L),117    EVNTDESC = case_when(118      DETER_EVENT ~ "PRO DETERIORATION",119      DEATH_EVENT ~ "DEATH",120      .default = "CENSORED"121    ),122    CNSDTDSC = case_when(123      !is.na(EVENTDT) ~ NA_character_,124      .default = coalesce(CENSORRSN, "STUDY COMPLETION")125    ),126    SRCDOM = case_when(127      DETER_EVENT ~ "QS",128      DEATH_EVENT ~ "ADSL",129      is.na(LASTQSLE) ~ "ADSL",130      .default = "QS"131    ),132    SRCVAR = case_when(133      DETER_EVENT ~ "ADT",134      DEATH_EVENT ~ "DTHDT",135      is.na(LASTQSLE) ~ "RANDDT",136      .default = "ADT"137    ),138    SRCSEQ = case_when(139      DETER_EVENT ~ DETERSEQ,140      is.na(EVENTDT) & !is.na(LASTQSLE) ~ LASTQSSEQ,141      .default = NA_integer_142    ),143    PARAMCD = "TTDGHS",144    PARAM = "Time to Deterioration in Global Health Status"145  ) |>146  select(147    STUDYID, USUBJID, PARAMCD, PARAM, STARTDT, ADT, AVAL, CNSR,148    EVNTDESC, CNSDTDSC, SRCDOM, SRCVAR, SRCSEQ149  ) |>150  arrange(USUBJID)151152dir.create("/app/output", showWarnings = FALSE)153write_csv(adtte, "/app/output/adtte.csv", na = "")

1# Reference solution for the yamaa benchmark adam-adtte-pro-deterioration (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 the ADTTE dataset (time to deterioration in global health status).89Reads ADSL, DS and QS from /app/input and writes /app/output/adtte.csv10with one record per subject.11"""1213import csv14import os15from datetime import date1617INPUT_DIR = "/app/input"18OUTPUT_DIR = "/app/output"1920CENSOR_REASONS = {21    "DISEASE PROGRESSION",22    "STUDY DISCONTINUATION",23    "WITHDRAWAL OF CONSENT",24}252627def parse_date(text):28    text = (text or "").strip()29    if not text:30        return None31    return date.fromisoformat(text[:10])323334def fmt(d):35    return d.isoformat() if d is not None else ""363738def whole_months(start, end):39    """Whole calendar months from start to end."""40    months = (end.year - start.year) * 12 + (end.month - start.month)41    if end.day < start.day:42        months -= 143    return months444546def read_csv(name):47    path = os.path.join(INPUT_DIR, name)48    with open(path, newline="", encoding="utf-8") as handle:49        return list(csv.DictReader(handle))505152def to_int(text, default=0):53    try:54        return int(float(text))55    except (TypeError, ValueError):56        return default575859def main():60    adsl = read_csv("adsl.csv")61    ds = read_csv("ds.csv")62    qs = read_csv("qs.csv")6364    ds_by_subject = {}65    for row in ds:66        ds_by_subject.setdefault(row["USUBJID"], []).append(row)6768    qs_by_subject = {}69    for row in qs:70        qs_by_subject.setdefault(row["USUBJID"], []).append(row)7172    out_rows = []73    for subj in adsl:74        usubjid = subj["USUBJID"]75        randdt = parse_date(subj.get("RANDDT"))76        dthdt = parse_date(subj.get("DTHDT"))7778        # Assessments with both a date and a score, in date/sequence order.79        assessments = []80        for row in qs_by_subject.get(usubjid, []):81            adt = parse_date(row.get("ADT"))82            score_text = (row.get("AVAL") or "").strip()83            if adt is None or not score_text:84                continue85            assessments.append(86                {87                    "date": adt,88                    "score": float(score_text),89                    "seq": to_int(row.get("QSSEQ")),90                }91            )92        assessments.sort(key=lambda a: (a["date"], a["seq"]))9394        # Deterioration: an assessment dated after the earliest assessment95        # whose score has fallen at least 10 points below that earliest96        # assessment's score; the earliest such assessment gives the date.97        deterioration = None98        if assessments:99            baseline = assessments[0]100            for a in assessments[1:]:101                if a["date"] > baseline["date"] and (102                    baseline["score"] - a["score"] >= 10103                ):104                    deterioration = a105                    break106107        # First censoring reason: earliest disposition record naming one of108        # the censoring reasons (never an event).109        censor_date = None110        censor_reason = ""111        records = []112        for row in ds_by_subject.get(usubjid, []):113            if (row.get("DSDECOD") or "").strip() in CENSOR_REASONS:114                records.append(115                    {116                        "date": parse_date(row.get("DSDTC")),117                        "seq": to_int(row.get("DSSEQ")),118                        "reason": (row.get("DSDECOD") or "").strip(),119                    }120                )121        records.sort(122            key=lambda r: (r["date"] is None, r["date"] or date.min, r["seq"])123        )124        if records:125            censor_date = records[0]["date"]126            censor_reason = records[0]["reason"]127128        def not_after_censor(d):129            return d is not None and (censor_date is None or d <= censor_date)130131        # Event selection: deterioration and death compete on date, with a132        # deterioration winning a same-date tie; each must not be dated133        # after the first censoring reason.134        event = None  # (kind, date, seq)135        candidates = []136        if deterioration is not None and not_after_censor(deterioration["date"]):137            candidates.append(("deterioration", deterioration["date"], 0))138        if dthdt is not None and not_after_censor(dthdt):139            candidates.append(("death", dthdt, 1))140        if candidates:141            candidates.sort(key=lambda c: (c[1], c[2]))142            kind, event_date, _ = candidates[0]143            if kind == "deterioration":144                event = ("deterioration", event_date, deterioration["seq"])145            else:146                event = ("death", event_date, None)147148        if event is not None:149            kind, adt, seq = event150            cnsr = 0151            cnsdtdsc = ""152            if kind == "deterioration":153                evntdesc = "PRO DETERIORATION"154                srcdom, srcvar, srcseq = "QS", "ADT", str(seq)155            else:156                evntdesc = "DEATH"157                srcdom, srcvar, srcseq = "ADSL", "DTHDT", ""158        else:159            cnsr = 1160            evntdesc = "CENSORED"161            cnsdtdsc = censor_reason if censor_reason else "STUDY COMPLETION"162            qualifying = [163                a164                for a in assessments165                if censor_date is None or a["date"] <= censor_date166            ]167            if qualifying:168                last = max(qualifying, key=lambda a: (a["date"], a["seq"]))169                adt = last["date"]170                srcdom, srcvar, srcseq = "QS", "ADT", str(last["seq"])171            else:172                adt = randdt173                srcdom, srcvar, srcseq = "ADSL", "RANDDT", ""174175        out_rows.append(176            {177                "STUDYID": subj["STUDYID"],178                "USUBJID": usubjid,179                "PARAMCD": "TTDGHS",180                "PARAM": "Time to Deterioration in Global Health Status",181                "STARTDT": fmt(randdt),182                "ADT": fmt(adt),183                "AVAL": str(whole_months(randdt, adt)),184                "CNSR": str(cnsr),185                "EVNTDESC": evntdesc,186                "CNSDTDSC": cnsdtdsc,187                "SRCDOM": srcdom,188                "SRCVAR": srcvar,189                "SRCSEQ": srcseq,190            }191        )192193    fieldnames = [194        "STUDYID",195        "USUBJID",196        "PARAMCD",197        "PARAM",198        "STARTDT",199        "ADT",200        "AVAL",201        "CNSR",202        "EVNTDESC",203        "CNSDTDSC",204        "SRCDOM",205        "SRCVAR",206        "SRCSEQ",207    ]208    os.makedirs(OUTPUT_DIR, exist_ok=True)209    with open(210        os.path.join(OUTPUT_DIR, "adtte.csv"), "w", newline="", encoding="utf-8"211    ) as handle:212        writer = csv.DictWriter(handle, fieldnames=fieldnames)213        writer.writeheader()214        writer.writerows(out_rows)215216217if __name__ == "__main__":218    main()

1/* opensas reference solution for the yamaa benchmark adam-adtte-pro-deterioration.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 DTHDT $1024;7  infile "/app/input/adsl.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDYID : $char1024. USUBJID : $char1024. RANDDT : $char1024. DTHDT : $char1024.;9run;1011data ds;12  length STUDYID USUBJID DSDECOD DSDTC $1024;13  infile "/app/input/ds.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;14  input STUDYID : $char1024. USUBJID : $char1024. DSDECOD : $char1024. DSDTC : $char1024. DSSEQ;15run;1617data qs;18  length STUDYID USUBJID AVISIT ADT $1024;19  infile "/app/input/qs.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;20  input STUDYID : $char1024. USUBJID : $char1024. QSSEQ AVISIT : $char1024. ADT : $char1024. AVAL;21run;2223proc sort data=qs(where=(ADT ne '')) out=ordered; by STUDYID USUBJID ADT QSSEQ; run;24data deteriorations;25  length BASEDT $10;26  retain BASEDT BASEVAL;27  set ordered; by STUDYID USUBJID;28  /* The baseline is the earliest dated assessment with a score; a scoreless29     row cannot be the baseline. */30  if first.USUBJID then do; BASEDT=''; BASEVAL=.; end;31  if missing(BASEDT) and not missing(AVAL) then do; BASEDT=ADT; BASEVAL=AVAL; end;32  if not missing(BASEDT) and ADT>BASEDT and not missing(AVAL) and AVAL<=BASEVAL-10;33run;34data deterioration; set deteriorations; by STUDYID USUBJID; if first.USUBJID; keep STUDYID USUBJID ADT QSSEQ; rename ADT=DETERDT QSSEQ=DETERSEQ; run;35data ds_order; set ds; NODATE=missing(DSDTC); run;36proc sort data=ds_order(where=(DSDECOD in ('DISEASE PROGRESSION','STUDY DISCONTINUATION','WITHDRAWAL OF CONSENT'))) out=reasons; by STUDYID USUBJID NODATE DSDTC DSSEQ; run;37data reason; set reasons; by STUDYID USUBJID; if first.USUBJID; keep STUDYID USUBJID DSDTC DSDECOD; rename DSDTC=REASONDT DSDECOD=REASON; run;38proc sql; create table assessment_reasons as select a.*,b.REASONDT from ordered as a left join reason as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID; quit;39data candidates; set assessment_reasons; if not missing(AVAL) and (missing(REASONDT) or ADT<=REASONDT); run;40proc sort data=candidates; by STUDYID USUBJID descending ADT descending QSSEQ; run;41data lastassessment; set candidates; by STUDYID USUBJID; if first.USUBJID; keep STUDYID USUBJID ADT QSSEQ; rename ADT=LASTDT QSSEQ=LASTSEQ; run;42proc sql; create table joined as select a.*,b.DETERDT,b.DETERSEQ,c.REASONDT,c.REASON,d.LASTDT,d.LASTSEQ from adsl as a43  left join deterioration as b on a.STUDYID=b.STUDYID and a.USUBJID=b.USUBJID left join reason 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;44data result;45  length PARAMCD $8 PARAM $60 STARTDT ADT $10 EVNTDESC CNSDTDSC $40 SRCDOM $4 SRCVAR $16;46  set joined; PARAMCD='TTDGHS'; PARAM='Time to Deterioration in Global Health Status'; STARTDT=RANDDT;47  if not missing(DETERDT) and (missing(DTHDT) or DETERDT<=DTHDT) and (missing(REASONDT) or DETERDT<=REASONDT) then do; ADT=DETERDT; CNSR=0; EVNTDESC='PRO DETERIORATION'; SRCDOM='QS'; SRCVAR='ADT'; SRCSEQ=DETERSEQ; end;48  else if not missing(DTHDT) and (missing(REASONDT) or DTHDT<=REASONDT) then do; ADT=DTHDT; CNSR=0; EVNTDESC='DEATH'; SRCDOM='ADSL'; SRCVAR='DTHDT'; end;49  else do;50    CNSR=1; EVNTDESC='CENSORED'; CNSDTDSC=coalescec(REASON,'STUDY COMPLETION');51    if not missing(LASTDT) then do; ADT=LASTDT; SRCDOM='QS'; SRCVAR='ADT'; SRCSEQ=LASTSEQ; end;52    else do; ADT=RANDDT; SRCDOM='ADSL'; SRCVAR='RANDDT'; end;53  end;54  if not missing(STARTDT) and not missing(ADT) then AVAL=intck('month',input(STARTDT,yymmdd10.),input(ADT,yymmdd10.),'continuous');55run;5657proc sql;58  create table final as select STUDYID, USUBJID, PARAMCD, PARAM, STARTDT, ADT, AVAL, CNSR, EVNTDESC, CNSDTDSC, SRCDOM, SRCVAR, SRCSEQ from result;59quit;60proc export data=final outfile="/app/output/adtte.csv" dbms=csv replace; run;