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clean-up

Jiho Noh romanegloo

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  • University of Kentucky
  • Lexington, KY
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@romanegloo
romanegloo / lucene_indexing.py
Created Feb 2, 2019
Indexing using PyLucene, example code
View lucene_indexing.py
'''
Indexing using PyLucene, example code
'''
import os
from pathlib import Path
import lucene
from java.nio.file import Paths
from org.apache.lucene.analysis.standard import StandardAnalyzer
@romanegloo
romanegloo / installation.md
Created Feb 2, 2019
PyLucene Installation
View installation.md

On Mac OS

Java

Both of Oracle Java 1.8 and Apple's Java 1.6 are required. You can download Oracle Java 1.8 from here.

For Apple's Java 1.6, download the package from here and install it.

View ukycs215_lab3.md

Lab 03

Schedule

  • Project 1 is due by Feb 8
  • Lab2 submission is due Tonight

Tips for Lab 03

How to print a float number with a fixed precision

ex) 41.4451 to 41.45

@romanegloo
romanegloo / BioASQ_questions_6b.txt
Created Jan 24, 2019
All the questions appeared in BioASQ 6b training data
View BioASQ_questions_6b.txt
"Is Hirschsprung disease a mendelian or a multifactorial disorder?"
"List signaling molecules (ligands) that interact with the receptor EGFR?"
"Is the protein Papilin secreted?"
"Are long non coding RNAs spliced?"
"Is RANKL secreted from the cells?"
"Does metformin interfere thyroxine absorption?"
"Which miRNAs could be used as potential biomarkers for epithelial ovarian cancer?"
"Which acetylcholinesterase inhibitors are used for treatment of myasthenia gravis?"
"Has Denosumab (Prolia) been approved by FDA?"
"List the human genes encoding for the dishevelled proteins?"
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
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
@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>
@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 / 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 / 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