Ming Hao minghao2016
minghao2016
/ run_python_script_in_conda_env.bat
Created
August 25, 2021 21:37
— forked from maximlt/run_python_script_in_conda_env.bat
Run a Python script in a conda environment from a batch file
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| @echo OFF | |
| rem How to run a Python script in a given conda environment from a batch file. | |
| rem It doesn't require: | |
| rem - conda to be in the PATH | |
| rem - cmd.exe to be initialized with conda init | |
| rem Define here the path to your conda installation | |
| set CONDAPATH=C:\ProgramData\Miniconda3 | |
| rem Define here the name of the environment |
minghao2016
/ custom-focal-loss-keras.R
Created
June 18, 2021 20:59
— forked from PsycheShaman/custom-focal-loss-keras.R
Custom Loss Function for R: Focal Loss (to Account for Imbalanced Classes During Classification), adapted from https://github.com/umbertogriffo/focal-loss-keras, since I could not find an equivalent loss function for R
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| require(keras) | |
| require(tensorflow) | |
| K <- keras::backend() | |
| # Custom Focal Loss | |
| focalLoss <- function(gamma=2., alpha=.25){ | |
minghao2016
/ Hello PyTorch.ipynb
Created
June 7, 2021 02:05
— forked from santi-pdp/Hello PyTorch.ipynb
Toy example in pytorch for binary classification
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
minghao2016
/ biotools_packages.txt
Created
February 12, 2021 19:19
— forked from dansondergaard/biotools_packages.txt
Package names from bio.tools and various conda channels (anaconda, conda-forge, bioconda, r).
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| KNIME - Cellular phenotyping | |
| Galaxy Image Analysis | |
| COMPSs | |
| YEASTRACT | |
| WormBase | |
| Reactome knowledgebase of biological pathways | |
| PRIDE | |
| PANTHER | |
| AnalysisServiceService | |
| Kyoto encyclopedia of genes and genomes KEGG |
minghao2016
/ plot_rf_tree.R
Created
November 6, 2020 18:32
— forked from sillasgonzaga/plot_rf_tree.R
Plot a tree from a Random Forest Model
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| plot_rf_tree <- function(final_model, tree_num, shorten_label = TRUE) { | |
| # source: https://shiring.github.io/machine_learning/2017/03/16/rf_plot_ggraph | |
| # get tree by index | |
| tree <- randomForest::getTree(final_model, | |
| k = tree_num, | |
| labelVar = TRUE) %>% | |
| tibble::rownames_to_column() %>% | |
| # make leaf split points to NA, so the 0s won't get plotted |
minghao2016
/ Tetherheavy.ipynb
Created
August 21, 2020 21:54
— forked from ptosco/Tetherheavy.ipynb
TetherHeavy
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
minghao2016
/ CanonicalReordering.ipynb
Created
August 19, 2020 01:58
— forked from ptosco/CanonicalReordering.ipynb
CanonicalReordering
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
minghao2016
/ GBDT_LR.py
Created
August 11, 2020 19:41
— forked from SS1031/GBDT_LR.py
GBDT-LogisticRegression
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| """ | |
| GBDT + LogisticRegression | |
| """ | |
| import numpy as np | |
| import matplotlib.pyplot as plt | |
| from matplotlib.colors import ListedColormap | |
| import seaborn as sns | |
| from sklearn.datasets import make_moons |
minghao2016
/ dbdt-lr-example.ipynb
Created
August 5, 2020 13:00
— forked from ianforme/dbdt-lr-example.ipynb
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
minghao2016
/ dockedpose.py
Created
July 29, 2020 14:33
— forked from baoilleach/dockedpose.py
Using Open Babel to calculate the symmetry-corrected RMSD of a docked pose from a crystal structure
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| import math | |
| import pybel | |
| def squared_distance(coordsA, coordsB): | |
| """Find the squared distance between two 3-tuples""" | |
| sqrdist = sum( (a-b)**2 for a, b in zip(coordsA, coordsB) ) | |
| return sqrdist | |
| def rmsd(allcoordsA, allcoordsB): | |
| """Find the RMSD between two lists of 3-tuples""" |
NewerOlder