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Level III

Machine Learning with XGBoost in a JMP Addin (JMP app + python)



I hope everyone's doing well in this time of great uncertainty


Here is an attempt of my first application built with app-builder using the connection between JMP and Python to handle a complex machine learning algorithm.

The purpose of this app is to launch a graphical user interface write in jsl and connect that interface with the “XGBoost” machine learning API.

I have implemented the possibility to work on 3 types of validation scheme: holdout / cross validation / grid search. Both regressions and classifications have been developed on few objectives and classical metrics.

At the end of the training, a report is supplied with metrics value on both train / validate set or on mean/standard dev for cross validation. In the case of a grid search training the report is supplied with best hyperparameters results and we can choose to use early stopping. It is possible too to export the python model to predict new datas without training the model again (but should be done in a python environment)


I hope it will work for everyone, I am not a professional software engineer and that app has been developed mainly during late night sessions but it seems OK on my computer in all tested configurations and classical dataset (titanic, boston houses,...) with that set up:

Numpy 1.18.1

Pandas 1.0.0

Scikitlearn 0.22.1

XGBoost 0.90

Python 3.7.5

And JMP 15.1 (in English, I do not have check in other languages…)


You should then check that JMP can handle that link with Python prior to use the app... Connecting Python to JMP is in fact not really straightforward and I advise you to contact JMP's support in case of problem because this integration is quite a nightmare for users in my point of view (in my case with a lot of JMP crashes without any warning or error messages before I succeed to make that working)


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Thanks for making this available! I am attempting to run it on the Boston Housing data, adjusted slightly to include an appropriate validation column and a numeric ID column and with the "chas" variable as a numeric indicator. (See screenshot below.) I am running JMP Pro 15.1 on MacOS 10.15.3 with Python 3.8.2 and numpy 1.18.2, pandas 1.0.3, scikit-learn 0.23.1, and XGBoost 1.1.0. I am copying the log below. Obviously something is working for a bit, but then Python crashes. In the end, I get the warning that "Send Expects Scriptable Object in access or evaluation of 'Send'." I imagine this error happens because Python crashed and didn't create the object to be sent.  


Any ideas on what might be going wrong? I'm no scripting expert, but in addition to this weakness, I don't comprehend the some of the French output in the log





"*** DEBUG Report: Start"
"******* Fonction update OK"
"**** Valeurs initialisées"
"**** OK avant lancement algo"
"***** La table de travail est:"
DataTable("Boston Housing.jmp")


# Partie import des biblios Python
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.metrics import mean_absolute_error
from sklearn.metrics import mean_squared_error
from xgboost import XGBRegressor
from joblib import dump, load
from pathlib import Path

# Optionnel
#from xgboost import plot_tree

# On affiche pas les warnings python
import warnings

	# On créé des DataFrame avec les Data Table JMP
	data_frame_train = pd.DataFrame(dt_train)
	data_frame_valid = pd.DataFrame(dt_valid)
	data_frame_test = pd.DataFrame(dt_test)

	# On récupère l'index du DF avec Id pour le réutiliser dans la génération du dataframe de la réponse
	Id_train = data_frame_train[colId]
	Id_valid = data_frame_valid[colId]
	Id_test = data_frame_test[colId]

	# On fixe l'index du DF avec Id

	# On conserve la table train non modifiée
	data_frame_train_initial = pd.DataFrame(dt_train)
	# On fixe l'index du DF avec Id

	# On fixe le y
	y_train = data_frame_train[colY]
	y_valid = data_frame_valid[colY]
	y_test = data_frame_test[colY]

	# On fixe les facteurs: ce sont ici les colonnes récupérées de la liste des colonnes de JMP donc les features contenus dans liste_colonne  

	X_train = data_frame_train[liste_colonne]
	X_valid = data_frame_valid[liste_colonne]
	X_test = data_frame_test[liste_colonne]


	# On définit le modèle comme étant un régresseur XGBoost 
	# my_model = XGBRegressor(n_estimators=100, learning_rate=0.05, random_state=0)

	#param_dist = {'n_estimators':2,'learning_rate'=0.05,'random_state'=0 }

	# ATTENTION: le transfert de variable est piégeux car un integer est converti en decimal
	# Or dans cette list de paramètre XGBoost ne tolère pas tout le temps des décimals, il faut donc convertir en Integer avec int()

	# Conversion des paramètres:
	Int_Nb_Iterations = int(Nb_Iterations)
	Int_Max_Depth = int (Max_Depth)
	Int_Min_Child = int (Min_Child)

	# Assignation des paramètres
	max_depth = Int_Max_Depth
	min_child_weight = Int_Min_Child
	subsample = Sub_Sample
	colsample_bytree = Col_Sample
	objective = Objective
	num_estimators = Int_Nb_Iterations
	learning_rate = Learning_Rate

	my_model = XGBRegressor(max_depth=max_depth,min_child_weight=min_child_weight,subsample=subsample,colsample_bytree=colsample_bytree,objective=objective,n_estimators=num_estimators,learning_rate=learning_rate)            

	# On fitte le modèle
	my_model.fit(X_train, y_train)

	# On récupère les prédictions sur le set de la table train partie validation
	predictions_sur_train_XGBoost = my_model.predict(X_train)
	predictions_sur_validation_XGBoost = my_model.predict(X_valid)

	# Calculate Score
	#score_train = mean_absolute_error(predictions_sur_train_XGBoost, y_train)
	#score_valid = mean_absolute_error(predictions_sur_validation_XGBoost, y_valid)

	if Type_Score == 'MAE': score_train = mean_absolute_error(predictions_sur_train_XGBoost, y_train); score_valid = mean_absolute_error(predictions_sur_validation_XGBoost, y_valid)
	elif Type_Score == 'RMSE': score_train = mean_squared_error(predictions_sur_train_XGBoost, y_train) ; score_valid = mean_squared_error(predictions_sur_validation_XGBoost, y_valid)
	else: print("toto")

	# Export prévisions sur table train et validate
	output_train_XGBoost = pd.DataFrame({colY: predictions_sur_train_XGBoost,colId : Id_train})
	output_validation_XGBoost = pd.DataFrame({colY: predictions_sur_validation_XGBoost, colId : Id_valid  })

	# On concatene les dataframe train et valid afin de réentrainer le modèle sur l'ensemble des données pour prédire le y_test
	X_full = pd.concat([X_train, X_valid])
	y_full = pd.concat([y_train, y_valid])

	# On réentraine le modèle sur train + validate et on l'exporte sur test
	my_model.fit(X_full, y_full)
	predictions_sur_test_XGBoost = my_model.predict(X_test)
	output_test_XGBoost = pd.DataFrame({colY: predictions_sur_test_XGBoost,colId : Id_test})

	# ------------------------- Essais de sortie graphique: plantage car JMP 15.1 n'est pas fonctionnel

	# fit = alg.fit(dtrain[ft_cols].values, dtrain['y'].values)
	# ft_weights = pd.DataFrame(fit.feature_importances_, columns=['weights'], index=ft_cols)

	# model = xgb.train(params, d_train, 1000, watchlist)
	# fig, ax = plt.subplots(figsize=(12,18))
	# xgb.plot_importance(model, max_num_features=50, height=0.8, ax=ax)
	# plt.show()

	# ft_weights = my_model.feature_importances_

	#import matplotlib.pylab as plt
	#from matplotlib import pyplot
	#from xgboost import plot_importance
	#plot_importance(model, max_num_features=10) # top 10 most important features

	# ------------------------- 

	if int(File_Save_Check) == 1:
		data_folder = Path(File_Save_Directory)
		file_to_save = data_folder / File_Save_Name
		dump(my_model, file_to_save) 

	print("python has crashed check your parameters")

Send Expects Scriptable Object in access or evaluation of 'Send' 

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Yes the problem is indeed in the python part sorry about that...

It is odd because the python code has not been executed at all: the code has crashed before the "try" command! I never add that kind of crash....

But it is tricky to debug your log because JMP doesn't write any of the python's error message... it just throw the python code without explanations... When we use python with JMP and python encounter a problem there is no explicit error code: I had to developped all the python code outside of JMP then integrate that code in JMP because of that...

This dataset is well handled on my computer but I work on windows 10 and with python 3.7



The first thing to check is that JMP 15.1 can handle python 3.8 I am really not sure it is the case (there was some difficulties with python 3.7 for example see https://community.jmp.com/t5/Discussions/JMP-14-Python-abilities-working-I-m-confused/td-p/184515 try to execute the example code in the scripting index:

Names Default To Here( 1 );
Python Init();
Python Submit(
str = 'The quick brown fox jumps over the lazy dog';
a = 200;
getStr = Python Get( str );
getNum = Python Get( a );
Show( getStr, getNum );
Python Term();


Then, is there any missing value in your data set ? (I do not check for missing value in the dataset and it can crash because of that if it is a reworked boston dataset with some missing values)

I am not sure too that my code can handle Mac OS because I have no way to check that and the python integration can be perhaps a bit different than windows... 

The same dataset with no problem on my computer:

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Thanks for looking at my issue, @Franck_R. My Python installation is working with JMP for other code (including the test code you suggested), but there may still be an issue with a package or some other missing component needed for your Add-In that I haven't yet discovered. I'm totally stumped for now. When I get a chance, I'll try setting this up on a Windows machine to give it another try. 


Thanks again for putting this out in the community -- it's a very useful application!

Hi Ruth

I am very sorry I have no clue on what's happening: I suspected some trouble with the way Mac OS handle directory differently that Windows but the crash is located in the python's part and not before that. Moreover the crash happens whereas you did not use the file export option

Perhaps it is related to a package issue as you mention. I will try to upgrade my packages as soon as possible to check if same packages on windows 10 are still OK or not. 

Thanks you for trying my addin ! 




This is great! Thanks for sharing* it


Regarding Python in Windows, Anaconda with Python 3.6 works out-of-the-box with JMP 15, but you need to update all the packages since it is a 2 y old package. I hope JMP improves their Python support in next versions.


(*note) The interface you have built can be used for other python APIs. Have you published the source code as well?



Thank you! 
Yes, I also hope that Python support will be improved over time.


For the interface, sorry I made this addin almost entirely on my free time but with JMP's licence paid by my company, I consider that the publication of the source code must be validated by my employer who wishes that this source code remains private.

No problem Franck. It is a great contribution, thanks for sharing.

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