I keep getting ValueError: Shapes (10, 1) and (10, 3) are incompatible when training my model

Turning the number of inputs when I call makeModel from 3 to 1 allows the program to run without errors but no training actually happens and the accuracy doesn’t change.

import pandas as pd
from numpy import loadtxt
from sklearn.impute import SimpleImputer
from sklearn.model_selection import train_test_split
from tensorflow.keras.models import Sequential
from tensorflow.keras.layers import Dense
from sklearn.preprocessing import LabelEncoder
from sklearn.utils import shuffle
from sklearn.tree import DecisionTreeRegressor as dtr
from sklearn.metrics import mean_absolute_error as mae
import numpy as np

def makeModel(num_inputs, num_classes, train_X, train_y):
    model = Sequential()
    model.add(Dense(8, input_dim=num_inputs, activation='relu'))
    model.add(Dense(10, activation='relu'))
    model.add(Dense(10, activation='relu'))
    model.add(Dense(10, activation='relu'))
    model.add(Dense(3, activation='softmax'))

    model.compile(loss='categorical_crossentropy', optimizer='adam', metrics=['accuracy'])
    model.fit(train_X, train_y, epochs=10, batch_size=10)

    return model

label_encoder = LabelEncoder()
iris_data = pd.read_csv("iris.csv")
iris_data = shuffle(iris_data)

iris_data['species'] = label_encoder.fit_transform(iris_data['species'])

feature_columns = ['sepal_length', 'sepal_width', 'petal_length', 'petal_width']

X = iris_data[feature_columns]
y = iris_data['species']

train_x, val_x, train_y, val_y = train_test_split(X, y, test_size=0.2)
iris_model = makeModel(4, 3, train_x, train_y)

Answer

LabelEncoder transforms the input to an array of encoded values. i.e if your input is ["paris", "paris", "tokyo", "amsterdam"] then they can be encoded as [0, 0, 1, 2]. It is not one-hot encoding scheme which is expected by categorical_crossentropy loss. If you have a integer encoding you will have to use sparse_categorical_crossentropy

Fix

change your code loss to sparse_categorical_crossentropy :

model.compile(loss='sparse_categorical_crossentropy', optimizer='adam', metrics=['accuracy'])

Sample

def makeModel(num_inputs, num_classes, train_X, train_y):
    model = Sequential()
    model.add(Dense(8, input_dim=num_inputs, activation='relu'))
    model.add(Dense(10, activation='relu'))
    model.add(Dense(10, activation='relu'))
    model.add(Dense(10, activation='relu'))
    model.add(Dense(3, activation='softmax'))

    model.compile(loss='sparse_categorical_crossentropy', optimizer='adam', metrics=['accuracy'])
    model.fit(train_X, train_y, epochs=10, batch_size=10)

    return model

label_encoder = LabelEncoder()
iris = datasets.load_iris()
y = iris.target
y = label_encoder.fit_transform(y)

train_x, val_x, train_y, val_y = train_test_split(iris.data, y, test_size=0.2)
iris_model = makeModel(4, 3, train_x, train_y)