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HiRID, a higher time-resolution icu dataset. Anonymization procedure

HiRID, a higher time-resolution icu dataset. Anonymization procedure

Posted Variation: 1.0


HiRID is really an easily accessible care that is critical containing data associated with very nearly 34 thousand patient admissions to your Department of Intensive Care Medicine regarding the Bern University Hospital, Switzerland (ICU), an interdisciplinary 60-bed product admitting >6,500 clients each year. The ICU provides the complete variety of contemporary interdisciplinary intensive care medication for adult clients. The dataset originated in cooperation amongst the Swiss Federal Institute of tech (ETH) ZГјrich, Switzerland in addition to ICU.

The dataset contains de-identified information that is demographic a total of 681 regularly gathered physiological factors, diagnostic test outcomes and therapy parameters from nearly 34 thousand admissions through the duration. Information is kept with a time that is uniquely high of just one entry every 2 minutes.


Critical disease is described as the existence or risk of developing organ dysfunction that is life-threatening. Critically sick clients are usually looked after in intensive care units (ICUs), which focus on supplying monitoring that is continuous advanced therapeutic and diagnostic technologies. This dataset had been gathered during routine care in the Department of Intensive Care Medicine for the Bern University Hospital, Switzerland (ICU), an interdisciplinary unit that is 60-bed >6,500 clients each year. It absolutely was initially removed to aid a research in the very very very early forecast of circulatory failure into the intensive care device machine learning 1 that is using. The latest paperwork for the dataset is available2.


The HiRID database includes a selection that is large of routinely gathered data relating to patient admissions towards the Department of Intensive Care Medicine associated with the Bern University Hospital, Switzerland (ICU). The information ended up being obtained through the ICU individual information Management System which can be accustomed register that is prospectively wellness information, dimensions of organ function parameters, outcomes of laboratory tests and treatment parameters from ICU admission to discharge.

Measurements from bedside monitoring

Dimensions and settings of medical products such as for example technical air flow

Findings by medical care providers e.g.: GCS, RASS, urine as well as other fluid production

Administered drugs, liquids and nourishment

HiRID has a greater time resolution than many other published datasets, above all for bedside monitoring with many parameters recorded every 120 seconds.

To guarantee the anonymization of an individual into the information set, we observed the procedures effectively applied for the MIMIC-IIwe and Amsterdam UMC db dataset, which adopted the ongoing health Insurance Portability and Accountability Act (HIPAA) secure Harbor needs and, when it comes to Amsterdam UMC db, additionally europe’s General information Protection Regulation (GDPR) standards 3,4.

Elimination of all eighteen data that are identifying placed in HIPAA

Times were shifted by a random offset in a way that the admission date lies. We ensured to protect the seasonality, time of time together with day’s week.

Individual age, height and fat are binned into containers of size 5. For patient age, the maximum container is 90 years possesses also all older clients.

Dimensions and medicines with changing devices in the long run had been standardised into the latest product utilized. This standardization had been essential to create a summary about projected admission times, on the basis of the devices utilized in a patient that is specific impossible.

Complimentary text had been taken from the database

k-anonymization ended up being used on patient age, fat, height and intercourse.

Ethical approval and client permission

The review that is institutional (IRB) associated with the Canton of Bern authorized the research. The necessity for acquiring informed client consent ended up being waived due to the retrospective and nature that is observational of research.

Information Description

The data that are overall obtainable in two states: as natural information and/or as pre-processed information. Also you will find three guide tables for adjustable lookup.

Guide tables

adjustable guide – guide dining dining table for factors (for natural stage)

ordinal adjustable guide – guide dining dining table for categorical/ordinal variables for string value lookup

pre-processed adjustable guide – guide dining dining dining table for factors (for merged and stage that is imputed

Natural information

The raw information was just prepared if this is necessary for patient de-identification and otherwise left unchanged when compared to source that is original. The origin information offers the complete pair of available factors (685 factors). It is comprised of the after tables:

Preprocessed information

The pre-processed information is made of intermediary pipeline phases from the accompanying book by Hyland et al 1. Supply factors representing exactly the same concepts that are clinical merged into one meta-variable per concept. The information provides the 18 many meta-variables that are predictive, as defined within our book. Two various phases associated with pipeline can be found

Merged phase supply factors are merged into meta-variables by medical ideas e.g. non-opioid-analgesics. The full time grid is kept unchanged and it is sparse.

Imputed phase the information through the merged stage is down sampled up to a time grid that is five-minute. Enough time grid is filled up with imputed values. The imputation strategy is complex and it is talked about within the initial book.

The rule utilized to create these phases are available in this GitHub repository under the preprocessing folder 5.

Which information to make use of?

The pre-processed information is intended primarily as being a fast method to jump-start a task or even for used in an a knockout post evidence of concept. We suggest utilizing the supply data whenever feasible for regular tasks. It’s the many flexible type and possesses the whole group of factors within the initial time quality.

Information platforms

Information is obtainable in two platforms: CSV for wide compatibility and Apache Parquet for performance and convenience.

Because the information sets are fairly big, these are generally put into partitions, such that they may be prepared in parallel in a simple method. The lookup dining dining table mapping patient id to partition id is provided within the file called combined with the information. The partitions are aligned involving the various information sets and tables, so that the info of an individual can invariably be located into the partition using the id that is same. Note however, that an individual may well not take place in all data sets, e.g. a patient could be lacking into the preprocessed information, because an individual did not meet with the demographic requirements become within the research.

Patient ID / ICU admission

The dataset treats each ICU admission uniquely which is extremely hard to spot numerous ICU admissions as originating from the patient that is same. For each ICU (re-)admission an original “Patient ID” is produced.

Information schemata

The schemata of each and every dining dining table are located in the *schemata.pdf* file.

Use Records

Whilst the database contains detailed information about the medical proper care of clients, it should be addressed with appropriate care and respect.

Scientists have to formally request access via PhysioNet. To be awarded access, the consumer needs to be described as a credentialed PhysioNet user, digitally signal the info Use Agreement and supply a particular research concern.

Conflicts of Interest

The authors declare no disputes of great interest


Access Policy: Only PhysioNet credentialed users who signal the specified DUA have access to the files.

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