Update README.md

README.md

@@ -1,24 +1,352 @@
----
---
---
- config_name: all_med_actions
  features:
  - name: ed_stay_id
    dtype: float64
  - name: subject_id
    dtype: int64
  - name: charttime
    dtype: timestamp[ns]
  - name: minutes_into_stay
    dtype: float64
  - name: drug_class
    dtype: string
  - name: action_idx
    dtype: int64
  - name: source
    dtype: string
  splits:
  - name: all_med_actions
    num_bytes: 93408141
    num_examples: 1235609
  download_size: 16415454
  dataset_size: 93408141
- config_name: combined_medication_features
  features:
  - name: ed_stay_id
    dtype: int64
  - name: subject_id
    dtype: int64
  - name: recon_ace_inhibitor
    dtype: uint8
  - name: recon_analgesic___nsaid
    dtype: uint8
  - name: recon_analgesic___opioid_nsaid
    dtype: uint8
  - name: recon_antiarrhythmic
    dtype: uint8
  - name: recon_antibiotic
    dtype: uint8
  - name: recon_anticoagulant
    dtype: uint8
  - name: recon_anticonvulsant
    dtype: uint8
  - name: recon_antiemetic
    dtype: uint8
  - name: recon_antiplatelet
    dtype: uint8
  - name: recon_antipsychotic
    dtype: uint8
  - name: recon_benzodiazepine___sedative_anxiolytic
    dtype: uint8
  - name: recon_beta_blocker
    dtype: uint8
  - name: recon_bronchodilator
    dtype: uint8
  - name: recon_calcium_channel_blocker
    dtype: uint8
  - name: recon_corticosteroid
    dtype: uint8
  - name: recon_diuretic
    dtype: uint8
  - name: recon_gi___acid_suppression
    dtype: uint8
  - name: recon_insulin_glucose
    dtype: uint8
  - name: recon_nitrate
    dtype: uint8
  - name: recon_n_total_meds
    dtype: uint16
  - name: recon_n_drug_classes
    dtype: uint8
  - name: edmeds_ace_inhibitor
    dtype: uint8
  - name: edmeds_analgesic___acetaminophen
    dtype: uint8
  - name: edmeds_analgesic___nsaid
    dtype: uint8
  - name: edmeds_analgesic___opioid_nsaid
    dtype: uint8
  - name: edmeds_antiarrhythmic
    dtype: uint8
  - name: edmeds_antibiotic
    dtype: uint8
  - name: edmeds_anticoagulant
    dtype: uint8
  - name: edmeds_anticonvulsant
    dtype: uint8
  - name: edmeds_antiemetic
    dtype: uint8
  - name: edmeds_antiplatelet
    dtype: uint8
  - name: edmeds_antipsychotic
    dtype: uint8
  - name: edmeds_benzodiazepine___sedative_anxiolytic
    dtype: uint8
  - name: edmeds_beta_blocker
    dtype: uint8
  - name: edmeds_bronchodilator
    dtype: uint8
  - name: edmeds_calcium_channel_blocker
    dtype: uint8
  - name: edmeds_corticosteroid
    dtype: uint8
  - name: edmeds_diuretic
    dtype: uint8
  - name: edmeds_gi___acid_suppression
    dtype: uint8
  - name: edmeds_iv_fluid
    dtype: uint8
  - name: edmeds_insulin_glucose
    dtype: uint8
  - name: edmeds_nitrate
    dtype: uint8
  - name: edmeds_other
    dtype: uint8
  - name: edmeds_n_dispenses
    dtype: uint16
  - name: edmeds_n_drug_classes
    dtype: uint8
  splits:
  - name: med_only
    num_bytes: 25173099
    num_examples: 399573
  download_size: 6049182
  dataset_size: 25173099
- config_name: ed_meds_timestep
  features:
  - name: ed_stay_id
    dtype: float64
  - name: subject_id
    dtype: int64
  - name: charttime
    dtype: timestamp[ns]
  - name: minutes_into_stay
    dtype: float64
  - name: drug_class
    dtype: string
  - name: action_idx
    dtype: int64
  - name: source
    dtype: string
  - name: __index_level_0__
    dtype: int64
  splits:
  - name: ed_meds_timestep
    num_bytes: 27076675
    num_examples: 323190
  download_size: 7130448
  dataset_size: 27076675
- config_name: empty_patient_state
  features:
  - name: subject_id
    dtype: int64
  - name: ed_stay_id
    dtype: int64
  - name: hadm_id
    dtype: float64
  - name: time_steps
    dtype: int64
  splits:
  - name: empty_patient_state
    num_bytes: 4324549602
    num_examples: 134616330
  download_size: 11217914
  dataset_size: 4324549602
- config_name: meds_admitted_er_actions
  features:
  - name: subject_id
    dtype: int64
  - name: stay_id
    dtype: int64
  - name: hadm_id
    dtype: float64
  - name: pyxis_charttime
    dtype: timestamp[ns, tz=UTC]
  - name: pyxis_med_rn
    dtype: float64
  - name: pyxis_medication
    dtype: string
  - name: emar_id
    dtype: 'null'
  - name: emar_charttime
    dtype: timestamp[ns, tz=UTC]
  - name: emar_medication
    dtype: 'null'
  - name: event_txt
    dtype: 'null'
  - name: scheduletime
    dtype: 'null'
  - name: in_er
    dtype: bool
  - name: medication
    dtype: string
  - name: drug_class
    dtype: string
  - name: action_time
    dtype: timestamp[ns]
  - name: ed_stay_id
    dtype: float64
  - name: ed_intime
    dtype: timestamp[ns]
  - name: minutes_into_stay
    dtype: float64
  - name: action_idx
    dtype: int64
  - name: __index_level_0__
    dtype: int64
  splits:
  - name: adm_er_clean
    num_bytes: 148079076
    num_examples: 912419
  download_size: 29150917
  dataset_size: 148079076
- config_name: vitals
  features:
  - name: ed_stay_id
    dtype: int64
  - name: subject_id
    dtype: int64
  - name: charttime
    dtype: timestamp[us]
  - name: temperature
    dtype: float64
  - name: heartrate
    dtype: float64
  - name: resprate
    dtype: float64
  - name: o2sat
    dtype: float64
  - name: sbp
    dtype: float64
  - name: dbp
    dtype: float64
  - name: pain
    dtype: large_string
  - name: time_since_last_hrs
    dtype: float64
  - name: temperature_rolling2h
    dtype: float64
  - name: temperature_delta
    dtype: float64
  - name: temperature_rate
    dtype: float64
  - name: heartrate_rolling2h
    dtype: float64
  - name: heartrate_delta
    dtype: float64
  - name: heartrate_rate
    dtype: float64
  - name: resprate_rolling2h
    dtype: float64
  - name: resprate_delta
    dtype: float64
  - name: resprate_rate
    dtype: float64
  - name: o2sat_rolling2h
    dtype: float64
  - name: o2sat_delta
    dtype: float64
  - name: o2sat_rate
    dtype: float64
  - name: sbp_rolling2h
    dtype: float64
  - name: sbp_delta
    dtype: float64
  - name: sbp_rate
    dtype: float64
  - name: dbp_rolling2h
    dtype: float64
  - name: dbp_delta
    dtype: float64
  - name: dbp_rate
    dtype: float64
  - name: pulse_pressure
    dtype: float64
  - name: map
    dtype: float64
  splits:
  - name: vitals
    num_bytes: 479613448
    num_examples: 1893713
  download_size: 84005509
  dataset_size: 479613448
- config_name: all_med_actions
  data_files:
  - split: all_med_actions
    path: modeling_data/all_med_actions-*
- config_name: combined_medication_features
  data_files:
  - split: med_only
    path: modeling_data/med_only-*
- config_name: ed_meds_timestep
  data_files:
  - split: ed_meds_timestep
    path: modeling_data/ed_meds_timestep-*
- config_name: empty_patient_state
  data_files:
  - split: empty_patient_state
    path: patient_state/*.parquet
- config_name: meds_admitted_er_actions
  data_files:
  - split: adm_er_clean
    path: modeling_data/adm_er_clean-*
- config_name: vitals
  data_files:
  - split: vitals
    path: vitals_triage/*.parquet
- config_name: height
  data_files:
  - split: height
    path: height/*.parquet
- config_name: weight
  data_files:
  - split: weight
    path: weight/*.parquet
---
-## empty_patient_state
-
-Empty data frame for patient state. Subject_id, ed_stay_id and hadm_id are retained for identification. A row is added for each 10 min time block for that unique stay
-
-**License:** PhysioNet Credentialed Health Data License 1.5.0 — https://physionet.org/content/mimiciv/view-license/3.1/
-
-## vitals
-
-Vitals cleaned using the same pattern and methods as the triage stats.  Rhythm was dropped. Triage stats were added for each ed stay Missing values were handled using forward fill then backward fill for the groups that did not have an initial value. Remaining NaN values were filled using Iterative Imputer from sci-kit learn.  Features were engineered for each vital to get a rolling 2h average, the delta from the most recent value, a time delta, rate of change, a general time delta, pulse pressure, and average perfusion pressure 
-
-**License:** PhysioNet Credentialed Health Data License 1.5.0 — https://physionet.org/content/mimiciv/view-license/3.1/
-
-## height
-
-Height and weight measurement records from hosp.omr for cohort patients — separated to take single measurements of height as an average of all available height measurements for a patient and retaining all separate weight measurements.  Duplicates were dropped Used to supplement ED and inpatient state features with recent baseline measurements.
-
-**License:** PhysioNet Credentialed Health Data License 1.5.0 — https://physionet.org/content/mimiciv/view-license/3.1/
-
-## weight
-
-Height and weight measurement records from hosp.omr for cohort patients — separated to take single measurements of height as an average of all available height measurements for a patient and retaining all separate weight measurements.  Duplicates were dropped Used to supplement ED and inpatient state features with recent baseline measurements.
-
-**License:** PhysioNet Credentialed Health Data License 1.5.0 — https://physionet.org/content/mimiciv/view-license/3.1/
+---
+{}
+---
+---
+license: other
+license_name: physionet-credentialed-health-data-1.5.0
+license_link: https://physionet.org/content/mimiciv/view-license/3.1/
+pretty_name: ADS599 Capstone Modeling Data — Empty Patient State
+dataset_info:
+- config_name: all_med_actions
+  features:
+  - name: ed_stay_id
+    dtype: float64
+  - name: subject_id
+    dtype: int64
+  - name: charttime
+    dtype: timestamp[ns]
+  - name: minutes_into_stay
+    dtype: float64
+  - name: drug_class
+    dtype: string
+  - name: action_idx
+    dtype: int64
+  - name: source
+    dtype: string
+  splits:
+  - name: all_med_actions
+    num_bytes: 93408141
+    num_examples: 1235609
+  download_size: 16415454
+  dataset_size: 93408141
+- config_name: combined_medication_features
+  features:
+  - name: ed_stay_id
+    dtype: int64
+  - name: subject_id
+    dtype: int64
+  - name: recon_ace_inhibitor
+    dtype: uint8
+  - name: recon_analgesic___nsaid
+    dtype: uint8
+  - name: recon_analgesic___opioid_nsaid
+    dtype: uint8
+  - name: recon_antiarrhythmic
+    dtype: uint8
+  - name: recon_antibiotic
+    dtype: uint8
+  - name: recon_anticoagulant
+    dtype: uint8
+  - name: recon_anticonvulsant
+    dtype: uint8
+  - name: recon_antiemetic
+    dtype: uint8
+  - name: recon_antiplatelet
+    dtype: uint8
+  - name: recon_antipsychotic
+    dtype: uint8
+  - name: recon_benzodiazepine___sedative_anxiolytic
+    dtype: uint8
+  - name: recon_beta_blocker
+    dtype: uint8
+  - name: recon_bronchodilator
+    dtype: uint8
+  - name: recon_calcium_channel_blocker
+    dtype: uint8
+  - name: recon_corticosteroid
+    dtype: uint8
+  - name: recon_diuretic
+    dtype: uint8
+  - name: recon_gi___acid_suppression
+    dtype: uint8
+  - name: recon_insulin_glucose
+    dtype: uint8
+  - name: recon_nitrate
+    dtype: uint8
+  - name: recon_n_total_meds
+    dtype: uint16
+  - name: recon_n_drug_classes
+    dtype: uint8
+  - name: edmeds_ace_inhibitor
+    dtype: uint8
+  - name: edmeds_analgesic___acetaminophen
+    dtype: uint8
+  - name: edmeds_analgesic___nsaid
+    dtype: uint8
+  - name: edmeds_analgesic___opioid_nsaid
+    dtype: uint8
+  - name: edmeds_antiarrhythmic
+    dtype: uint8
+  - name: edmeds_antibiotic
+    dtype: uint8
+  - name: edmeds_anticoagulant
+    dtype: uint8
+  - name: edmeds_anticonvulsant
+    dtype: uint8
+  - name: edmeds_antiemetic
+    dtype: uint8
+  - name: edmeds_antiplatelet
+    dtype: uint8
+  - name: edmeds_antipsychotic
+    dtype: uint8
+  - name: edmeds_benzodiazepine___sedative_anxiolytic
+    dtype: uint8
+  - name: edmeds_beta_blocker
+    dtype: uint8
+  - name: edmeds_bronchodilator
+    dtype: uint8
+  - name: edmeds_calcium_channel_blocker
+    dtype: uint8
+  - name: edmeds_corticosteroid
+    dtype: uint8
+  - name: edmeds_diuretic
+    dtype: uint8
+  - name: edmeds_gi___acid_suppression
+    dtype: uint8
+  - name: edmeds_iv_fluid
+    dtype: uint8
+  - name: edmeds_insulin_glucose
+    dtype: uint8
+  - name: edmeds_nitrate
+    dtype: uint8
+  - name: edmeds_other
+    dtype: uint8
+  - name: edmeds_n_dispenses
+    dtype: uint16
+  - name: edmeds_n_drug_classes
+    dtype: uint8
+  splits:
+  - name: med_only
+    num_bytes: 25173099
+    num_examples: 399573
+  download_size: 6049182
+  dataset_size: 25173099
+- config_name: ed_meds_timestep
+  features:
+  - name: ed_stay_id
+    dtype: float64
+  - name: subject_id
+    dtype: int64
+  - name: charttime
+    dtype: timestamp[ns]
+  - name: minutes_into_stay
+    dtype: float64
+  - name: drug_class
+    dtype: string
+  - name: action_idx
+    dtype: int64
+  - name: source
+    dtype: string
+  - name: __index_level_0__
+    dtype: int64
+  splits:
+  - name: ed_meds_timestep
+    num_bytes: 27076675
+    num_examples: 323190
+  download_size: 7130448
+  dataset_size: 27076675
+- config_name: empty_patient_state
+  features:
+  - name: subject_id
+    dtype: int64
+  - name: ed_stay_id
+    dtype: int64
+  - name: hadm_id
+    dtype: float64
+  - name: time_steps
+    dtype: int64
+  splits:
+  - name: empty_patient_state
+    num_bytes: 4324549602
+    num_examples: 134616330
+  download_size: 11217914
+  dataset_size: 4324549602
+- config_name: meds_admitted_er_actions
+  features:
+  - name: subject_id
+    dtype: int64
+  - name: stay_id
+    dtype: int64
+  - name: hadm_id
+    dtype: float64
+  - name: pyxis_charttime
+    dtype: timestamp[ns, tz=UTC]
+  - name: pyxis_med_rn
+    dtype: float64
+  - name: pyxis_medication
+    dtype: string
+  - name: emar_id
+    dtype: 'null'
+  - name: emar_charttime
+    dtype: timestamp[ns, tz=UTC]
+  - name: emar_medication
+    dtype: 'null'
+  - name: event_txt
+    dtype: 'null'
+  - name: scheduletime
+    dtype: 'null'
+  - name: in_er
+    dtype: bool
+  - name: medication
+    dtype: string
+  - name: drug_class
+    dtype: string
+  - name: action_time
+    dtype: timestamp[ns]
+  - name: ed_stay_id
+    dtype: float64
+  - name: ed_intime
+    dtype: timestamp[ns]
+  - name: minutes_into_stay
+    dtype: float64
+  - name: action_idx
+    dtype: int64
+  - name: __index_level_0__
+    dtype: int64
+  splits:
+  - name: adm_er_clean
+    num_bytes: 148079076
+    num_examples: 912419
+  download_size: 29150917
+  dataset_size: 148079076
+- config_name: vitals
+  features:
+  - name: ed_stay_id
+    dtype: int64
+  - name: subject_id
+    dtype: int64
+  - name: charttime
+    dtype: timestamp[us]
+  - name: temperature
+    dtype: float64
+  - name: heartrate
+    dtype: float64
+  - name: resprate
+    dtype: float64
+  - name: o2sat
+    dtype: float64
+  - name: sbp
+    dtype: float64
+  - name: dbp
+    dtype: float64
+  - name: pain
+    dtype: large_string
+  - name: time_since_last_hrs
+    dtype: float64
+  - name: temperature_rolling2h
+    dtype: float64
+  - name: temperature_delta
+    dtype: float64
+  - name: temperature_rate
+    dtype: float64
+  - name: heartrate_rolling2h
+    dtype: float64
+  - name: heartrate_delta
+    dtype: float64
+  - name: heartrate_rate
+    dtype: float64
+  - name: resprate_rolling2h
+    dtype: float64
+  - name: resprate_delta
+    dtype: float64
+  - name: resprate_rate
+    dtype: float64
+  - name: o2sat_rolling2h
+    dtype: float64
+  - name: o2sat_delta
+    dtype: float64
+  - name: o2sat_rate
+    dtype: float64
+  - name: sbp_rolling2h
+    dtype: float64
+  - name: sbp_delta
+    dtype: float64
+  - name: sbp_rate
+    dtype: float64
+  - name: dbp_rolling2h
+    dtype: float64
+  - name: dbp_delta
+    dtype: float64
+  - name: dbp_rate
+    dtype: float64
+  - name: pulse_pressure
+    dtype: float64
+  - name: map
+    dtype: float64
+  splits:
+  - name: vitals
+    num_bytes: 479613448
+    num_examples: 1893713
+  download_size: 84005509
+  dataset_size: 479613448
+configs:
+- config_name: all_med_actions
+  data_files:
+  - split: all_med_actions
+    path: modeling_data/all_med_actions-*
+- config_name: combined_medication_features
+  data_files:
+  - split: med_only
+    path: modeling_data/med_only-*
+- config_name: ed_meds_timestep
+  data_files:
+  - split: ed_meds_timestep
+    path: modeling_data/ed_meds_timestep-*
+- config_name: empty_patient_state
+  data_files:
+  - split: empty_patient_state
+    path: patient_state/*.parquet
+- config_name: meds_admitted_er_actions
+  data_files:
+  - split: adm_er_clean
+    path: modeling_data/adm_er_clean-*
+- config_name: vitals
+  data_files:
+  - split: vitals
+    path: vitals_triage/*.parquet
+---
+
+
+
+## empty_patient_state
+
+
+
+
+
+Empty data frame for patient state. Subject_id, ed_stay_id and hadm_id are retained for identification. A row is added for each 10 min time block for that unique stay
+
+
+
+
+
+**License:** PhysioNet Credentialed Health Data License 1.5.0 — https://physionet.org/content/mimiciv/view-license/3.1/
+
+
+
+
+
+## vitals
+
+
+
+
+
+Vitals cleaned using the same pattern and methods as the triage stats.  Rhythm was dropped. Triage stats were added for each ed stay Missing values were handled using forward fill then backward fill for the groups that did not have an initial value. Remaining NaN values were filled using Iterative Imputer from sci-kit learn.  Features were engineered for each vital to get a rolling 2h average, the delta from the most recent value, a time delta, rate of change, a general time delta, pulse pressure, and average perfusion pressure 
+
+
+
+
+
+**License:** PhysioNet Credentialed Health Data License 1.5.0 — https://physionet.org/content/mimiciv/view-license/3.1/
+