false.alarm

PhD Programme in Health Data Science - detecting life-threatening ECG patterns using low-end devices

https://github.com/franzbischoff/false.alarm

Science Score: 36.0%

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codemeta.json file
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Low similarity (15.8%) to scientific vocabulary

Keywords

ecg matrix-profile signal-processing time-series

Last synced: 6 months ago · JSON representation

Repository

PhD Programme in Health Data Science - detecting life-threatening ECG patterns using low-end devices

Basic Info

Host: GitHub
Owner: franzbischoff
License: other
Language: HTML
Default Branch: master
Homepage: https://franzbischoff.github.io/false.alarm/
Size: 1.7 GB

Statistics

Stars: 6
Watchers: 1
Forks: 2
Open Issues: 17
Releases: 4

Topics

ecg matrix-profile signal-processing time-series

Created almost 6 years ago · Last pushed 9 months ago

Metadata Files

Readme License Codemeta

README.Rmd

---
title: "Detecting life-threatening patterns in Point-of-care ECG using efficient memory and processor power."
author: "Francisco Bischoff"
date: "on `r format(Sys.time(), '%B %d, %Y')`"
bibliography: [./papers/references.bib]
link-citations: true
csl: ./thesis/csl/ama.csl
editor_options:
  markdown:
    mode: markdown
output: github_document
always_allow_html: true
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
knitr::opts_knit$set(progress = TRUE, verbose = TRUE)
suppressPackageStartupMessages(library(tibble))
suppressPackageStartupMessages(library(kableExtra))
```



[![Gitpod Ready-to-Code](https://img.shields.io/badge/Gitpod-Ready--to--Code-blue?logo=gitpod)](https://gitpod.io/#https://github.com/franzbischoff/false.alarm/tree/develop) [![Launch binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/franzbischoff/false.alarm/master?urlpath=rstudio)
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[![](https://zenodo.org/badge/261530912.svg)](https://zenodo.org/badge/latestdoi/261530912)
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[![Language grade: C/C++](https://img.shields.io/lgtm/grade/cpp/g/franzbischoff/false.alarm.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/franzbischoff/false.alarm/context:cpp)




# Abstract

Currently, Point-of-Care (POC) ECG monitoring works either as plot devices or alarms for abnormal cardiac rhythms using
predefined normal trigger ranges and some rhythm analysis, which raises the problem of false alarms. In comparison,
complex 12-derivation ECG machines are not suitable to use as simple monitors and are used with strict techniques for
formal diagnostics. We aim to identify, on streaming data, life-threatening hearth electric patterns to reduce the
number of false alarms, using low CPU and memory maintaining robustness. The study design is comparable to a diagnostic
study, where high accuracy is essential. Physionet's 2015 challenge yielded very good algorithms for reducing false
alarms. However, none of the authors reported benchmarks, memory usage, robustness test, or context invariance that
could assure its implementation on real monitors to reduce alarm fatigue indeed. We expect to identify the obstacles of
detecting life-threatening ECG changes within memory, space, and CPU constraints and to reduce ECG monitor's false
alarms using the proposed methodology, and assess the feasibility of implementing the algorithm in the real world and
other settings than ICU monitors.

The research team is well experienced in time-series and has studied the Matrix Profile since its beginning, being
founders of the Matrix Profile Foundation whose goal is to have a concise and stable cross-language API for developing
with the Matrix Profile technology. [@Bischoff2019a; @VanBenschoten2020]

# Related Works

The CinC/Physionet Challenge 2015 produced several papers aiming to reduce false alarms on their dataset. On the
following table it is listed the five life-threatening alarms present in their dataset.

```{r alarms, echo=FALSE}
alarms <- tribble(
  ~Alarm, ~Definition,
  "Asystole", "No QRS for at least 4 seconds",
  "Extreme Bradycardia", "Heart rate lower than 40 bpm for 5 consecutive beats",
  "Extreme Tachycardia", "Heart rate higher than 140 bpm for 17 consecutive beats",
  "Ventricular Tachycardia", "5 or more ventricular beats with heart rate higher than 100 bpm",
  "Ventricular Flutter/Fibrillation", "Fibrillatory, flutter, or oscillatory waveform for at least 4 seconds"
)

kbl(alarms, booktabs = TRUE, caption = "Definition of the 5 alarm types used in CinC/Physionet Challenge 2015 challenge.", align = "ll") |>
  kable_styling(full_width = TRUE) |>
  column_spec(1, width = "5cm") |>
  row_spec(0, bold = TRUE)
```

# About the ongoing project

The document submitted for approval is
[here](https://github.com/franzbischoff/false.alarm/blob/master/protocol/Protocol.pdf).

To follow the thesis timeline you can access the full Gantt chart at Zenhub. Click
[here](https://app.zenhub.com/workspaces/phd-thesis-5eb2ce34f5f30b3aed0a35af/roadmap) (you need a github account, but
that's it).

# Reproducible Research[@krystalli_2019]

This thesis will follow the compendium principles:

![](docs/figure/compendium_principles.png)

![](docs/figure/compendium_principles2.png)

## Following Standards

Aiming to create secure materials that are [FAIR](https://www.nature.com/articles/sdata201618) *findable, accessible,
interoperable, reusable*

### Research Data Management

-   [**RDM
    checklist**](http://www.dcc.ac.uk/sites/default/files/documents/resource/DMP/DMP_Checklist_2013.pdf)[@dcc_2013]
-   Anticipate **data products** as part of your thesis **outputs**
-   Think about what technologies to use

### Missing values are a fact of life

-   Usually, best solution is to **leave blank**
-   **`NA`** or **`NULL`** are also good options
-   **NEVER use `0`**. Avoid numbers like **`-999`**
-   Don't make up your own code for missing values

### Raw data are sacrosanct

-   Don't, not even with a barge pole, not for one second, touch or otherwise edit the raw data files. Do an
    manipulations in script

### Three principles for good (file) names

#### Machine readable

-   Regular expression and globbing friendly

    -   Avoid spaces, punctuation, accented characters, case sensitivity

-   Easy to compute on

    -   Deliberate use of delimiters

    -   Deliberate use of `"-"` and `"_"` allows recovery of metadata from the filenames:

        -   `"_"` underscore used to delimit units of metadata I want to access later

        -   `"-"` hyphen used to delimit words so our eyes don't bleed

#### Human readable

-   Borrowing the concept from [slugs](https://en.wikipedia.org/wiki/Clean_URL#Slug) from semantic URLs

#### Play well with default ordering

-   Put something numeric first

-   Use the ISO 8601 standard for dates

-   Left pad other numbers with zeros

# License



[![Creative Commons
License](https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png)](https://creativecommons.org/licenses/by-nc-sa/4.0/)



This work is licensed under a [Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International
License](https://creativecommons.org/licenses/by-nc-sa/4.0/).

# Package dependencies



```{r dependency_plot, echo = FALSE, fig.width = 16, fig.height = 10, message = FALSE, warning = FALSE, fig.path = "man/figures/"}
devtools::source_gist("3b83243dfdfa73e459935112f3f783e3", filename = "plot_dependencies.R", sha1 = "a0ff78da8ddf58a4129abb89498abb90ca91738b", quiet = TRUE)
plot_dependencies()
```



# References

Owner

Name: Francisco Bischoff
Login: franzbischoff
Kind: user
Location: Portugal
Company: RISE-Health @ up.pt

Website: https://rise-health.pt/home_en/
Twitter: franzbischoff
Repositories: 194
Profile: https://github.com/franzbischoff

Researcher at RISE-Health / Faculty of Medicine, University of Porto

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  "developmentStatus": "https://www.repostatus.org/#wip",
  "keywords": [
    "ecg",
    "signal-processing",
    "time-series",
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  ]
}

GitHub Events

Total

Issues event: 11
Watch event: 1
Issue comment event: 1
Push event: 4

Last Year

Issues event: 11
Watch event: 1
Issue comment event: 1
Push event: 4

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Last synced: 12 months ago

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Total issues: 181
Total pull requests: 9
Average time to close issues: 3 months
Average time to close pull requests: 17 days
Total issue authors: 4
Total pull request authors: 2
Average comments per issue: 0.06
Average comments per pull request: 0.44
Merged pull requests: 5
Bot issues: 97
Bot pull requests: 9

Past Year

Issues: 7
Pull requests: 0
Average time to close issues: N/A
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Average comments per pull request: 0
Merged pull requests: 0
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mend-bolt-for-github[bot] (52)
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Mend: dependency security vulnerability (52) Epic (18) enhancement (2) documentation (1) todo :spiral_notepad: (1)

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dependencies (4)

Dependencies

DESCRIPTION cran

R >= 4.2 depends
Rcpp >= 1.0.6 imports
RcppParallel >= 5.1.4 imports
bookdown >= 0.22 imports
checkmate >= 2.0.0 imports
future >= 1.24.0 imports
ggplot2 >= 3.3.5 imports
glue >= 1.6.2 imports
gridExtra >= 2.3 imports
here >= 0.1.0 imports
kableExtra >= 1.3.4 imports
plotly >= 4.9.3 imports
purrr >= 0.3.4 imports
rmarkdown >= 2.12.2 imports
tarchetypes >= 0.4.1 imports
targets >= 0.2.0 imports
thesisdown >= 0.1.9 imports
tibble >= 3.1.6 imports
tidymodels >= 0.1.4 imports
visNetwork >= 2.1.0 imports
workflowr >= 1.6.2 imports
yardstick >= 0.0.9 imports
DT >= 0.18 suggests
clustermq >= 0.8.95 suggests
codemetar >= 0.3.3 suggests
covr >= 3.5.1 suggests
debugme >= 1.0.0 suggests
future >= 1.21.0 suggests
ggnetwork >= 0.5.10 suggests
gittargets >= 0.0.3 suggests
jsonld >= 2.2 suggests
jsonlite >= 1.8.0 suggests
knitr >= 1.33 suggests
languageserver >= 0.3.12 suggests
lintr >= 2.0.1 suggests
matrixprofiler >= 0.1.7 suggests
miniCRAN >= 0.2.16 suggests
progress >= 1.2.2 suggests
rlang >= 1.0.2 suggests
spelling >= 2.0.0 suggests
styler >= 1.6.2 suggests
testthat >= 3.1.3 suggests
tsmp >= 0.4.14 suggests
usethis >= 2.1.5 suggests

.github/workflows/R-CMD-check.yaml actions

actions/cache v2.1.4 composite
actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite

.github/workflows/binder.yaml actions

jupyterhub/repo2docker-action master composite

.github/workflows/ci.yaml actions

actions/cache v2.1.4 composite
actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-tinytex v2 composite

.github/workflows/codeql-analysis.yaml actions

actions/cache v2.1.4 composite
actions/checkout v2 composite
actions/upload-artifact main composite
github/codeql-action/analyze v1 composite
github/codeql-action/init v1 composite
r-lib/actions/setup-r v2 composite

.github/workflows/test-coverage.yaml actions

actions/cache v2.1.4 composite
actions/checkout v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite

.devcontainer/Dockerfile docker

base latest build
branch-${flavor} latest build
ubuntu focal build

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