Skip to content

Instantly share code, notes, and snippets.

View romanegloo's full-sized avatar
😀
clean-up

Jiho Noh romanegloo

😀
clean-up
  • University of Kentucky
  • Lexington, KY
View GitHub Profile
@romanegloo
romanegloo / 331-bm-acronyms.csv
Last active November 2, 2018 13:56
331 Most common biomedical abbreviations found in Medline abstracts
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
@romanegloo
romanegloo / spacy_multithreading_example.py
Created December 12, 2018 22:08
Multithreading spaCy's parser
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 December 28, 2018 15:16
Uninstall a Python version and reinstall a new oone

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 December 28, 2018 16:42
LaTeX frequently used examples

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 December 29, 2018 20:15
Evaluation Datasets for Word Embeddings

Evaluation Datasets for Word Embeddings

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 January 9, 2019 15:20
lab1 note for UKY CS 215

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 January 11, 2019 19:25
TREC precision medicine document samples
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 January 11, 2019 19:33
TREC clinical decision support track --- sample topic
<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>
@romanegloo
romanegloo / sta580_final_review.md
Created January 11, 2019 19:43
STA580 fianl review

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
@romanegloo
romanegloo / sta580_midterm_review.md
Created January 11, 2019 19:44
STA580 midterm review

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