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@staceysv
staceysv / protein_ligand_train.py
Created May 6, 2021 18:12
basic wandb integration for deepchem protein-ligand tutorial
View protein_ligand_train.py
#! /usr/bin/env python
import deepchem as dc
from deepchem.utils import download_url
from deepchem.utils.evaluate import Evaluator
import pandas as pd
import nglview
import tempfile
import os
@staceysv
staceysv / mol_sol_sweep.yaml
Created May 6, 2021 18:07
sweep config for molecular solubility deepchem tutorial
View mol_sol_sweep.yaml
name: dnn cling test
project: deepchem_molsol
description: go deeper and wider on FC net
program: ml_train.py
method: bayes
metric:
name: r2
goal: maximize
parameters:
batch_size:
@staceysv
staceysv / mol_sol_train.py
Created May 6, 2021 17:59
basic script to log deepchem molecular solubility tutorial to wandb
View mol_sol_train.py
# mol_sol_train.py
#--------------
# Load molecular solubility dataset, featurize, train FC net regression model,
# and evaluate by R^2 score.
import deepchem as dc
from deepchem.utils.evaluate import Evaluator
from deepchem.utils.save import load_from_disk
import numpy as np
import numpy.random
@staceysv
staceysv / composite_histogram.json
Created August 24, 2020 23:46
Custom Vega spec for a composite histogram plot in wandb
View composite_histogram.json
{
"$schema": "https://vega.github.io/schema/vega/v5.json",
"padding": 5,
"signals": [
{
"name": "binOffset",
"value": 0
},
{
"name": "binStep",
@staceysv
staceysv / prepare_miniimagenet.py
Last active April 10, 2020 17:39
organize mini-ImageNet files for MAML training
View prepare_miniimagenet.py
#!/usr/bin/env python
import csv
from PIL import Image
import pickle
import os
img_size = 84
test_csv_file = "../../Code/few-shot-ssl-public/fewshot/data/mini_imagenet_split/Ravi/test.csv"
train_csv_file = "../../Code/few-shot-ssl-public/fewshot/data/mini_imagenet_split/Ravi/train.csv"
@staceysv
staceysv / distributed_training.py
Created February 25, 2020 20:33
data-parallel distributed training in Keras with wandb
View distributed_training.py
import argparse
import time
import os
import tensorflow
from tensorflow.keras import optimizers
from tensorflow.keras.preprocessing.image import ImageDataGenerator
from tensorflow.keras.models import Sequential
from tensorflow.keras.layers import Conv2D, MaxPooling2D
@staceysv
staceysv / adv_finetune.py
Created October 2, 2019 21:39
finetune Keras model, log precision with custom W&B callback
View adv_finetune.py
from keras.preprocessing import image
from keras.models import Model
from keras.layers import Dense, GlobalAveragePooling2D
from keras.preprocessing.image import ImageDataGenerator
from keras import backend as K
import wandb
from wandb.keras import WandbCallback
from keras_callbacks import PerClassMetrics
@staceysv
staceysv / keras_callbacks.py
Last active October 2, 2019 21:36
example W&B callback for per-class precision
View keras_callbacks.py
from keras.callbacks import Callback
import numpy as np
import pandas
from sklearn.metrics import precision_score
import time
import wandb
# other metrics from sklearn we may use
# confusion_matrix, f1_score, recall_score