Skip to content

Instantly share code, notes, and snippets.

Avatar
😀
clean-up

Jiho Noh romanegloo

😀
clean-up
  • University of Kentucky
  • Lexington, KY
View GitHub Profile
@romanegloo
romanegloo / 331-bm-acronyms.csv
Last active Nov 2, 2018
331 Most common biomedical abbreviations found in Medline abstracts
View 331-bm-acronyms.csv
frequency abbreviation phrase
50580 MRI magnetic resonance imaging
48054 BMI body mass index
45890 CT computed tomography
42919 NO nitric oxide
42320 ROS reactive oxygen species
42072 PCR polymerase chain reaction
41060 AD Alzheimer's disease
35266 LPS lipopolysaccharide
35101 IL interleukin
View spacy_multithreading_example.py
import spacy
nlp = spacy.load('de')
for doc in nlp.pipe(texts, n_threads=16, batch_size=10000):
analyse_text(doc)
@romanegloo
romanegloo / reinstall_python.md
Last active Dec 28, 2018
Uninstall a Python version and reinstall a new oone
View reinstall_python.md

On Mac OS, managing Python versions with homebrew is not trivial, almost impossible.

Here, I uninstall pre-installed python version and re-install a new specific version.

To Uninstall a Python3 version

    ls -l /usr/local/bin | grep /Library/Frameworks/Python.framework/Versions/3 | awk '{print "rm \47/usr/local/bin/" $9 "\47"}'
    ls -d /Library/Frameworks/Python.framework/Versions/3.* 2> /dev/null | awk '{print "rm -rf \47" $0 "\47"}'
@romanegloo
romanegloo / latex_template.md
Last active Dec 28, 2018
LaTeX frequently used examples
View latex_template.md

nice table

\begin{table*}[!htbp]
  \centering
  \ra{1.3}
  \subfloat[Results on year 2016 datasets]{
    \begin{tabular}{@{}lcrrrrrcrrrrr@{}}
      \toprule
      \multirow{2}{*}{Models} & & \multicolumn{5}{c}{Optimized ARS weights} &&
      \multicolumn{5}{c}{MAP} \\
@romanegloo
romanegloo / we_eval_sets.md
Last active Dec 29, 2018
Evaluation Datasets for Word Embeddings
View we_eval_sets.md

Evaluation Datasets for Word Embeddings

SimVerb-3500 [download]

semantic similarity of verbs

[sample]

hurt    offend          V       6.81    SYNONYMS
clarify worry           V       0.33    NONE
fasten  attach          V       8.47    HYPER/HYPONYMS
@romanegloo
romanegloo / ukycs215_lab1.md
Last active Jan 9, 2019
lab1 note for UKY CS 215
View ukycs215_lab1.md

Environment

prefer NO (fancy) IDE like VS, XCode, Clion... I prefer plain text files

How to compile C++ file and Run

compile

g++ [source file] -o [executable file]
@romanegloo
romanegloo / clinical_trial-sample.xsd
Last active Jan 11, 2019
TREC precision medicine document samples
View clinical_trial-sample.xsd
public.xsd:
<?xml version="1.0" encoding="UTF-8" ?>
<!-- ============================================================================================
XML Schema for ClinicalTrials.gov public XML
http://clinicaltrials.gov/ct2/html/images/info/public.xsd
National Library of Medicine, National Institutes of Health
@romanegloo
romanegloo / gist:9d2b8b8c50fed2de716a9913d905dc89
Created Jan 11, 2019
TREC clinical decision support track --- sample topic
View gist:9d2b8b8c50fed2de716a9913d905dc89
<description>A 15 yo girl accompanied by her mother is referred for evaluation by the school. The girl has more than expected absences in the last three month, appears to be constantly tired and sleepy in class. Her mother assures the girl is well fed, and getting the proper sleep at night but admits the girls tires easily when they go out on weekend hikes. Physical examination: BP: 90/60. HR 130/min the only remarkable findings are extremely pale skin and mucosae. Grade 3/6 systolic murmur. Lab tests report Hb: 4.2 g/dL, MCV 61.8 fL, serum iron less than 1.8 umol/L and ferritin of 2 ng/mL. Fecal occult blood is negative.</description>
<summary>A 15 yo girl with fatigue, pale skin, low hemoglobin and ferritin.</summary>
<diagnosis>Iron-Deficiency Anemia</diagnosis>
<target>treatment</target>
View sta580_final_review.md

STA580 final summary

ANOVA (analysis of variance)

  • testing whether the means of two or more populations are equal
  • must have a continuous response and at least one categorical factor

one-way ANOVA

  • one fixed factor
View sta580_midterm_review.md

STA 580 midterm summary

Lecture 1 - Numerical and graphical summaries of data

  • graphical measures and plots
  • measure of location
    • mean (x_bar)
    • median
  • measure of dispersion
    • variance