{"id":3512,"date":"2023-08-31T11:12:58","date_gmt":"2023-08-31T11:12:58","guid":{"rendered":"https:\/\/neuraldesigner.com\/learning\/palmer-penguins\/"},"modified":"2025-09-15T17:24:08","modified_gmt":"2025-09-15T15:24:08","slug":"palmer-penguins","status":"publish","type":"learning","link":"https:\/\/www.neuraldesigner.com\/learning\/examples\/palmer-penguins\/","title":{"rendered":"Classify Palmer penguins using machine learning"},"content":{"rendered":"<section><\/section>\n<p>This example builds a machine learning model to classify size measurements for adult foraging penguins near Palmer Station, Antarctica.<\/p>\n<p>We used data on 11 variables obtained during penguin sampling in Antarctica.<\/p>\n<p>This data is obtained from the <a href=\"https:\/\/allisonhorst.github.io\/palmerpenguins\/\">palmerpenguins package<\/a>.<\/p>\n<section>This example is solved with <a href=\"https:\/\/www.neuraldesigner.com\/\">Neural Designer<\/a>. We recommend you follow it step by step using the <a href=\"https:\/\/www.neuraldesigner.com\/free-trial\">free trial<\/a>.<\/p>\n<h3>Contents<\/h3>\n<ol>\n<li><a href=\"#ApplicationType\">Application type<\/a>.<\/li>\n<li><a href=\"#DataSet\">Data set<\/a>.<\/li>\n<li><a href=\"#NeuralNetwork\">Neural network<\/a>.<\/li>\n<li><a href=\"#TrainingStrategy\">Training strategy<\/a>.<\/li>\n<li><a href=\"#TestingAnalysis\">Testing analysis<\/a>.<\/li>\n<li><a href=\"#ModelDeployment\">Model deployment<\/a>.<\/li>\n<\/ol>\n<\/section>\n<section id=\"ApplicationType\">\n<h2>1. Application type<\/h2>\n<p>The predicted variable can have three values corresponding to a penguin species: Adelie, Gentoo, and Chinstrap. Therefore, this is a multiple <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/neural-networks-applications#Classification\">classification<\/a> project.<\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.neuraldesigner.com\/images\/penguin_culmen_depth.webp\" \/><\/p>\n<p>The goal of this example is to model the probability of each sample belonging to a penguin species.<\/p>\n<\/section>\n<section id=\"DataSet\">\n<h2>2. Data set<\/h2>\n<h3>Data source<\/h3>\n<p>The <a href=\"https:\/\/www.neuraldesigner.com\/wp-content\/uploads\/2023\/10\/penguin_dataset.csv\">penguin_dataset.csv<\/a> file contains the data for this example.<\/p>\n<p>Target variables have three values in our classification model: Adelie (0), Gentoo (1), and Chinstrap (2).<\/p>\n<p>The number of rows (instances) in the data set is 334, and the number of variables (columns) is 11.<\/p>\n<h3>Variables<\/h3>\n<p>The following list summarizes the <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/data-set#Variables\">variables&#8217;<\/a> information:<\/p>\n<ul>\n<li><b>clutch_completion<\/b>: a character string denoting if the study nest was observed with a full clutch, i.e., 2 eggs.<\/li>\n<li><span style=\"box-sizing: border-box; margin: 0px; padding: 0px;\"><strong>date_egg<\/strong>: a date denoting the date the study nest was observed with 1 egg (sampled).<\/span><\/li>\n<li><b>culmen_length_mm<\/b>: a number denoting the length of the dorsal ridge of a bird&#8217;s bill (millimeters).<\/li>\n<li><b>culmen_depth_mm<\/b>: a number denoting the depth of the dorsal ridge of a bird&#8217;s bill (millimeters).<\/li>\n<li><span style=\"box-sizing: border-box; margin: 0px; padding: 0px;\"><strong>flipper_length_mm<\/strong>: an integer denoting the length of the penguin&#8217;s flipper (millimeters).<\/span><\/li>\n<li><b>body_mass_g<\/b>: an integer denoting the penguin&#8217;s body mass (grams).<\/li>\n<li><b>sex<\/b>: a factor denoting penguin sex (female, male).<\/li>\n<li><b>delta_15_N<\/b>: a number denoting the measure of the ratio of stable isotopes 15N:14N.<\/li>\n<li><b>delta_13_C<\/b>: a number denoting the measure of the ratio of stable isotopes 13C:12C.<\/li>\n<\/ul>\n<p>The number of <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/data-set#InputVariables\">input variables<\/a>, or attributes for each sample, is 9.<\/p>\n<p>The number of <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/data-set#TargetVariables\">target variables<\/a> is 1, species (adelie, gentoo, and chinstrap).<\/p>\n<h3>Instances<\/h3>\n<p>Each row contains the input and target variables of a different <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/data-set#Instances\">instance<\/a>.<\/p>\n<div class=\"text-base my-auto mx-auto pb-10 [--thread-content-margin:--spacing(4)] thread-sm:[--thread-content-margin:--spacing(6)] thread-lg:[--thread-content-margin:--spacing(16)] px-(--thread-content-margin)\">\n<div class=\"[--thread-content-max-width:40rem] thread-sm:[--thread-content-max-width:40rem] thread-lg:[--thread-content-max-width:48rem] mx-auto max-w-(--thread-content-max-width) flex-1 group\/turn-messages focus-visible:outline-hidden relative flex w-full min-w-0 flex-col agent-turn\" tabindex=\"-1\">\n<div class=\"flex max-w-full flex-col grow\">\n<div class=\"min-h-8 text-message relative flex w-full flex-col items-end gap-2 text-start break-words whitespace-normal [.text-message+&amp;]:mt-5\" dir=\"auto\" data-message-author-role=\"assistant\" data-message-id=\"478e0e43-e5ba-4435-8eb7-cf1e5dc3eef5\" data-message-model-slug=\"gpt-5\">\n<div class=\"flex w-full flex-col gap-1 empty:hidden first:pt-[3px]\">\n<div class=\"markdown prose dark:prose-invert w-full break-words light markdown-new-styling\">\n<p data-start=\"0\" data-end=\"213\" data-is-last-node=\"\" data-is-only-node=\"\">The dataset is divided into training, validation, and testing subsets.<\/p>\n<p data-start=\"0\" data-end=\"213\" data-is-last-node=\"\" data-is-only-node=\"\">By default, Neural Designer assigns 60% for training, 20% for validation, and 20% for testing, but you can adjust these percentages as needed.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<h3>Variables distributions<\/h3>\n<p>Also, we can calculate the <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/data-set#Distributions\">distributions<\/a> of all variables. The following pie chart shows the number of species we have.<\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.neuraldesigner.com\/images\/penguin_species_distribution.webp\" \/><\/p>\n<p>The image shows the proportion of each penguin species: Adelie (44.18%), Gentoo (36,04%), and Chinstrap (19.76%).<\/p>\n<h3>Inputs-targets correlations<\/h3>\n<p>The <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/data-set#InputsTargetsCorrelations\">input-target correlations<\/a> might indicate which factors most differentiate between penguins and, therefore, be more relevant to our analysis.<\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.neuraldesigner.com\/images\/penguin_correlations.webp\" \/><\/p>\n<p>Here, the most correlated variables with penguin species are <b>date_egg<\/b>, <b>culmen_depth_mm<\/b>, <b>delta_13_C,<\/b> and <b>delta_15_N<\/b>.<\/p>\n<\/section>\n<h2>3. Neural network<\/h2>\n<p>The next step is to set a <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/neural-network\">neural network<\/a> as the classification function. Usually, the neural network is composed of:<\/p>\n<ul>\n<li><a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/neural-network#ScalingLayer\">Scaling layer<\/a>.<\/li>\n<li><a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/neural-network#PerceptronLayers\">Dense layer<\/a>.<\/li>\n<li><a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/neural-network#ProbabilisticLayer\">Probabilistic layer<\/a>.<\/li>\n<\/ul>\n<h3>Scaling layer<\/h3>\n<p>The <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/neural-network#ScalingLayer\">scaling layer<\/a> contains the inputs scaled from the data file and the method used for scaling. Here, the method selected is the <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/neural-network#MinimumMaximumScalingMethod\">minimum-maximum<\/a>. As we use ten input variables, the scaling layer has ten inputs.<\/p>\n<h3>Dense layer<\/h3>\n<p id=\"NeuralNetwork\">The <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/neural-network#ProbabilisticLayer\">dense layer<\/a> applies the Softmax activation to interpret outputs as class probabilities.<\/p>\n<p>It takes ten inputs and produces three outputs.<\/p>\n<p>Each output gives the probability of a sample belonging to a class.<\/p>\n<h3>Neural network graph<\/h3>\n<p>The following figure represents the neural network:<\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.neuraldesigner.com\/images\/penguin_network.webp\" \/><\/p>\n<p>The network takes ten inputs and produces three outputs, which represent the probability of a penguin belonging to a given class.<\/p>\n<section id=\"TrainingStrategy\">\n<h2>4. Training strategy<\/h2>\n<p>The fourth step is to set the <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/training-strategy\">training strategy<\/a>, which is composed of two terms:<\/p>\n<ul>\n<li>A loss index.<\/li>\n<li>An optimization algorithm.<\/li>\n<\/ul>\n<h3>Loss index<\/h3>\n<p>The aim is to find a neural network that fits the data set (<a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/training-strategy#ErrorTerm\">error term<\/a>) and does not oscillate (<a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/training-strategy#RegularizationTerm\">regularization term<\/a>).<\/p>\n<p>The <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/training-strategy#LossIndex\">loss index<\/a> is the <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/training-strategy#NormalizedSquaredError\">normalized squared error<\/a> with <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/training-strategy#L2Regularization\">L2 regularization<\/a>, the default loss index for classification applications.<\/p>\n<h3>Optimization algorithm<\/h3>\n<p>The <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/training-strategy#OptimizationAlgorithm\">optimization algorithm<\/a> we use is the <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/training-strategy#QuasiNewtonMethod\">quasi-Newton method<\/a>, the standard optimization algorithm for this type of problem.<\/p>\n<h3>Training<\/h3>\n<p>The following image shows how the error decreases with the iterations during the training process.<\/p>\n<p><img decoding=\"async\" src=\"https:\/\/www.neuraldesigner.com\/images\/penguin_error.webp\" \/><\/p>\n<p>The curves have converged, as we can see in the previous image.<\/p>\n<p>The final errors are 0.004 for training and 0.005 for validation.<\/p>\n<p>However, the selection error is a bit higher than the training error.<\/p>\n<\/section>\n<section id=\"ModelSelection\"><\/section>\n<section id=\"TestingAnalysis\">\n<h2>6. Testing analysis<\/h2>\n<p>The objective of the <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/testing-analysis\">testing analysis<\/a> is to validate the generalization properties of the trained neural network.<\/p>\n<p>The method to validate the performance of our model is to compare the predicted values to the real values, using a confusion matrix.<\/p>\n<h3>Confusion matrix<\/h3>\n<p>The rows represent the real classes in the confusion matrix, and the columns are the predicted classes for the testing data.<\/p>\n<p>The following table contains the values of the confusion matrix.<\/p>\n<style type=\"text\/css\">\n                .tg {<br \/>                    border-collapse: collapse;<br \/>                    border-spacing: 0;<br \/>                }<\/p>\n<p>                    .tg td {<br \/>                        border-color: black;<br \/>                        border-style: solid;<br \/>                        border-width: 1px;<br \/>                        font-size: 14px;<br \/>                        overflow: hidden;<br \/>                        padding: 10px 5px;<br \/>                        word-break: normal;<br \/>                    }<\/p>\n<p>                    .tg th {<br \/>                        border-color: black;<br \/>                        border-style: solid;<br \/>                        border-width: 1px;<br \/>                        font-size: 14px;<br \/>                        font-weight: normal;<br \/>                        overflow: hidden;<br \/>                        padding: 10px 5px;<br \/>                        word-break: normal;<br \/>                    }<\/p>\n<p>                    .tg .tg-baqh {<br \/>                        text-align: center;<br \/>                        vertical-align: top<br \/>                    }<\/p>\n<p>                    .tg .tg-6qw1 {<br \/>                        background-color: #c0c0c0;<br \/>                        text-align: center;<br \/>                        vertical-align: top<br \/>                    }<\/p>\n<p>                    .tg .tg-u1yq {<br \/>                        background-color: #c0c0c0;<br \/>                        font-weight: bold;<br \/>                        text-align: center;<br \/>                        vertical-align: top<br \/>                    }<br \/>            <\/style>\n<table>\n<thead>\n<tr>\n<th><\/th>\n<th>Predicted Adelie<\/th>\n<th>Predicted Gentoo<\/th>\n<th>Predicted Chinstrap<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td>Real Adelie<\/td>\n<td>22 (32.353%)<\/td>\n<td>0<\/td>\n<td>1 (1.471%)<\/td>\n<\/tr>\n<tr>\n<td>Real Gentoo<\/td>\n<td>0<\/td>\n<td>31 (45.588%)<\/td>\n<td>1 (1.471%)<\/td>\n<\/tr>\n<tr>\n<td>Real Chinstrap<\/td>\n<td>0<\/td>\n<td>0<\/td>\n<td>13 (19.118%)<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>As we can see, we can classify 66 (97.1%) of the samples, while we fail to do so for 2 (2.9%) samples<\/p>\n<\/section>\n<section id=\"ModelDeployment\">\n<h2>7. Model deployment<\/h2>\n<p>Once we have tested the neural network&#8217;s performance, we can save it for the future using the <a href=\"https:\/\/www.neuraldesigner.com\/learning\/tutorials\/model-deployment\">model deployment<\/a> mode.<\/p>\n<\/section>\n<section>\n<h2>References<\/h2>\n<ul>\n<li>Artwork by <a href=\"https:\/\/twitter.com\/allison_horst\">@allison_horst<\/a><\/li>\n<li>This data is obtained from the <a href=\"https:\/\/allisonhorst.github.io\/palmerpenguins\/\">palmerpenguins package<\/a><\/li>\n<li>Gorman KB, Williams TD, Fraser WR (2014). Ecological sexual dimorphism and environmental variability within a community of Antarctic penguins (genus Pygoscelis). <a href=\"https:\/\/doi.org\/10.1371\/journal.pone.0090081\">PLoS ONE 9(3):e90081<\/a>.<\/li>\n<li>GitHub: <a href=\"https:\/\/allisonhorst.github.io\/palmerpenguins\/\">Palmerpenguins<\/a><\/li>\n<\/ul>\n<\/section>\n<section>\n<h2>Related examples<\/h2>\n<\/section>\n","protected":false},"author":19,"featured_media":1742,"template":"","categories":[29],"tags":[46],"class_list":["post-3512","learning","type-learning","status-publish","has-post-thumbnail","hentry","category-examples","tag-environment"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.4 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Classify Palmer penguins using machine learning<\/title>\n<meta name=\"description\" content=\"Build a machine learning model to classify measurements of adult penguins foraging near Palmer Station, Antarctica.\" \/>\n<meta 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