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Internal transfers are counted as readmissions

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  • ¿Algo no está bien?
#1,269 3 comentarios 0 reacciones 0 asignados Ver en GitHub

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@thebean27 ya está trabajando en esto.

Desde el 6/10/2026.

  • #1275 de @thebean27 — abierto

Evaluación

Dificultad
4/5
Tiempo estimado
3-5 días
Aptitud para principiantes
35/100
Tipo de issue
Error
Claridad
Bastante claro
Estado de actividad
Estancado
Stack tecnológico
python
Área
data

Línea de trabajo

The issue provides a reproducer using admissions.csv.gz and points to the prior exclusion clause removed in PR #815; start by tracing the readmission-label logic and reviewing PR #815 and the open PR #1275. Compare how admissions less than an hour apart are labeled with the intended treatment of internal transfers. Done means the behavior is addressed or its intended configuration is clarified, with tests covering the relevant case.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

Hi, first of all thank you for your repo; it has been useful for my research and very easy to use.

I have found an issue wherein internal transfers are counted as readmissions rather than treated as part of the same visit; which I think is surprising and probably not what most people want to model.

Reproduce (needs only admissions.csv.gz)

import polars as pl
pl.Config.set_fmt_str_lengths(60)   # print full admission_location strings

adm = (
    pl.read_csv("data/mimiciv/3.1/hosp/admissions.csv.gz", try_parse_dates=True)
       .sort("subject_id", "admittime")
       .with_columns(
              next_admit=pl.col("admittime").shift(-1).over("subject_id"),
              next_loc=pl.col("admission_location").shift(-1).over("subject_id")
       )
       .filter(pl.col("next_admit").is_not_null())
)
gap = pl.col("next_admit") - pl.col("dischtime")
pos = adm.filter(gap < pl.duration(days=30))          # the task's label rule
split = pos.filter(gap < pl.duration(hours=1))

print("total 30-day readmissions:", len(pos))     # 110k
print("readmissions within 1hr:  ", len(split))   # 10k (~9%)

# second admisison_location
print(split["next_loc"].value_counts(sort=True).head(5))
# ┌────────────────────────────────────────┬───────┐
# │ next_loc                               ┆ count │
# │ ---                                    ┆ ---   │
# │ str                                    ┆ u32   │
# ╞════════════════════════════════════════╪═══════╡
# │ INTERNAL TRANSFER TO OR FROM PSYCH     ┆ 5609  │
# │ PHYSICIAN REFERRAL                     ┆ 1844  │
# │ EMERGENCY ROOM                         ┆ 1451  │
# │ TRANSFER FROM SKILLED NURSING FACILITY ┆ 535   │
# │ WALK-IN/SELF REFERRAL                  ┆ 103   │
# └────────────────────────────────────────┴───────┘

Possibly related to https://patch-diff.githubusercontent.com/raw/sunlabuiuc/PyHealth/pull/815.diff
which removed a clause excluding admissions within 3hrs of a prev. admission.

-                if time_diff_hour <= 3:
-                    continue

A possible fix could be to merge admissions occuring within some time period and adding that as a configuration option and to emit some warning suggesting user's configure that value. I would imagine waiting for a major version change to change the default behaviour would be a good idea.

Environment: PyHealth 2.0.2, MIMIC-IV 3.1.

Lenguaje dominante
Python
Estrellas
1.7k
Forks
803
Merge medio
5 d 16 h
PR fusionados (30 d)
58

Preparar el entorno

Primeros pasos

  1. Lee el issue completo y luego la guía de contribución del proyecto.
  2. Comenta en el issue que vas a ocuparte — evita que dos personas hagan lo mismo.
  3. Haz un fork del repositorio y trabaja en una rama.
  4. Abre un pull request que haga referencia al número del issue.

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