Last week Blaž, Marko and I held a week long introductory Data Mining and Machine Learning course at the Ljubljana Doctoral Summer School 2018. We got a room full of dedicated students and we embarked on a journey through standard and advanced machine learning techniques, all presented of course in Orange. We have covered a wide array of topics, from different clustering techniques (hierarchical clustering, k-means) to predictive models (logistic regression, naive Bayes, decision trees, random forests), regression and regularization, projections, text mining and image analytics.
Definitely the biggest crowd-pleaser was the Geo add-on in combination with the HDI data set. First, we got the HDI data from Datasets. A quick glimpse into a data table to check the output. We have information on some key performance indicators gathered by the United Nations for 188 countries. Now we would like to know which countries are similar based on the reported indicators. We will use Distances with Euclidean distance and use Ward linkage in Hierarchical Clustering.
We got our results in a dendrogram. Interestingly, the United States seems similar to Cuba. Let us select this cluster and inspect what the most significant feature for this cluster. We will use the Data output of Hierarchical Clustering which append a column indicating whether the data instances was selected or not. Then we will use Box Plot, group by Selected and check Order by relevance. It seems like these countries have the longest life expectancy at age 59. Go ahead and inspect other clusters by yourself!
Of course, when we are talking about countries one naturally wants to see them on a map! That is easy. We will use the Geo add-on. First, we need to convert all the country names to geographical coordinates. We will do this with Geocoding, where we will encode column Country to latitude and longitude. Remember to use the same output as before, that is Data to Data.
Now, let us display these countries on a map with Choropleth widget. Beautiful. It is so easy to explore country data, when you see it on a map. You can try coloring also by HDI or any other feature.
The final workflow:
We always try to keep our workshops fresh and interesting and visualizations are the best way to achieve this. Till the next workshop!
This week we held our first Girls Go Data Mining workshop. The workshop brought together curious women and intuitively introduced them to essential data mining and machine learning concepts. Of course, we used Orange to explore visualizations, build predictive models, perform clustering and dive into text analysis. The workshop was supported by NumFocus through their small development grant initiative and we hope to repeat it next year with even more ladies attending!
In two days, we covered many topics. On day one, we got to know Orange and the concept of visual programming, where the user construct analytical workflow by stacking visual components. Then we got to know several useful visualizations, such as box plot, scatter plot, distributions, and mosaic display, which give us an initial overview of the data and the potentially interesting patterns. Finally, we got our hands dirty with predictive modeling. We learnt about decision trees, logistic regression, and naive Bayes classifiers, and observed the models in tree viewer and nomogram. It is great having interpretable models and we had great fun exploring what is in the model!
On the second day, we tried to uncover groups in our data with clustering. First, we tried hierarchical clustering and explored the discovered clusters with box plot. Then we also tried k-means and learnt, why this method is better than hierarchical clustering. In the final part, we talked about the methods for text mining, how to do preprocessing, construct a bag of words and perform the machine learning on corpora. We used both clustering and classification and tried to find interesting information about Grimm tales.
One thing that always comes up as really useful in our workshops is Orange’s ability to output different types of data. For example, in Hierarchical Clustering, we can select the similarity cutoff at the top and output clusters. Our data table will have an additional column Cluster, with cluster labels for each data instance.
We can explore clusters by connecting a Box Plot to Hierarchical Clustering, selecting Cluster in Subgroups and using Order by relevance option. This sorts the variables in Box Plot by how well they separate between clusters or, in other words, what is typical of each cluster.
We used zoo.tab and made the cutoff at three clusters. It looks like the first cluster gives milk. Could these be a cluster of mammals?
Indeed it is!
Another option is to select a specific cluster in the dendrogram. Then, we have to rewire the connection between Hierarchical Clustering and Box Plot by setting it to Data. Data option will output the entire data set, with an extra column showing whether the data instance was selected or not. In our case, there would be a Yes if the instance is in the selected cluster and No if it is not.
Then we can use Box Plot to observe what is particular for our selected cluster.
It looks like animals from our selected cluster have feathers. Probably, this is a cluster of birds. We can check this with the same procedure as above.
In summary, most Orange visualizations have two outputs – Selected Data and Data. Selected Data will output a subset of data instances selected in the visualization (or selected clusters in the case of hierarchical clustering), while Data will output the entire data table with a column defining whether a data instance was selected or not. This is very useful if we want to inspect what is typical of an interesting group in our data, inspect clusters or even manually define groups.
Overall, this was another interesting workshop and we hope to continue our fruitful partnership with NumFocus and keep offering free educational events for beginners and experts alike!
Janez and I have recently returned from a two-week stay in Moscow, Russian Federation, where we were teaching data mining to MA students of Applied Statistics. This is a new Master’s course that attracts the best students from different backgrounds and teaches them statistical methods for work in the industry.
It was a real pleasure working at HSE. The students were proactive by asking questions and really challenged us to do our best.
One of the things we did was compute minimum cost of misclassifications. The story goes like this. Sara is a doctor and has data on 303 patients with heart disease (Orange’s heart-disease.tab data set). She used some classifiers and now has to decide how many patients to send for further tests. Naive Bayes classifier, for example, returned probabilities of a patient being sick (column Naive Bayes 1). For each threshold in probabilites, she will compute how many false positives (patients declared sick when healthy) and how many false negatives (patients declared healthy when sick) a classifiers returns. Each mistake is associated with a cost. Now she wants to find out, how many patients to send for tests (what probability threshold to choose) so that her cost is the lowest.
First, import all the libraries we will need:
import matplotlib.pyplot as plt
import numpy as np
from Orange.data import Table
from Orange.classification import NaiveBayesLearner, TreeLearner
from Orange.evaluation import CrossValidation
Then load heart disease data (and print a sample).
heart = Table("heart_disease")
Now, train classifiers and select probabilities of Naive Bayes for a patient being sick.
scores = CrossValidation(heart, [NaiveBayesLearner(), TreeLearner()])
#take probabilites of class 1 (sick) of NaiveBayesLearner
p1 = scores.probabilities[:, 1]
#take actual class values
y = scores.actual
#cost of false positive (patient classified as sick when healthy)
fp_cost = 500
#cost of false negative (patient classified as healthy when sick)
fn_cost = 800
Set counts, where we declare 0 patients being sick (threshold >1).
fp = 0
#start with threshold above 1 (no one is sick)
fn = np.sum(y)
For each threshold, compute the cost associated with each type of mistake.
ps = 
costs = 
#compute costs of classifying i patients as sick
for i in np.argsort(p1)[::-1]:
if y[i] == 0:
fp += 1
fn -= 1
costs.append(fp * fp_cost + fn * fn_cost)
In the end, we get a list of probability thresholds and associated costs. Now let us find the minimum cost and its probability of a patient being sick.
costs = np.array(costs)
#find probability of a patient being sick at lowest cost
This means the threshold that minimizes our cost for a given classifier is 0.620655. Sara would send all the patients with a probability of being sick higher or equal than 0.620655 for further tests.
At the end, we can also plot the cost to patients sent curve.
Two days ago we held another Introduction to Data Mining workshop at our faculty. This time the target audience was a group of public sector professionals and our challenge was finding the right data set to explain key data mining concepts. Iris is fun, but not everyone is a biologist, right? Fortunately, we found this really nice data set with ballot counts from the Slovenian National Assembly (thanks to Parlameter).
The data contains ballot counts, statistics, and description for 84 members of the parliament (MPs). First, we inspected the data in a Data Table. Each MP is described with 14 meta features and has 18 ballot counts recorded.
We have some numerical features, which means we can also inspect the data in Scatter Plot. We will plot MPs’ attendance vs. the number of their initiatives. Quite interesting! There is a big group of MPs who regularly attend the sessions, but rarely propose changes. Could this be the coalition?
The next question that springs to our mind is – can we discover interesting voting patterns from our data? Let us see. We first explored the data in Hierarchical Clustering. Looks like there are some nice clusters in our data! The blue cluster is the coalition, red the SDS party and green the rest (both from the opposition).
But it is hard to inspect so many data instances in a dendrogram. For example, we have no idea how similar are the voting records of Eva Irgl and Alenka Bratušek. Surely, there must be a better way to explore similarities and perhaps verify that voting patterns exist at even a party-level… Let us try MDS. MDS transforms multidimensional data into a 2D projection so that similar data instances lie close to each other.
Ah, this is nice! We even colored data points by the party. MDS beautifully shows the coalition (blue dots) and the opposition (all other colors). Even parties are clustered together. But there are some outliers. Let us inspect Matej Tonin, who is quite far away from his orange group. Seems like he was missing at the last two sessions and did not vote. Hence his voting is treated differently.
It is always great to inspect discovered groups and outliers. This way an expert can interpret the clusters and also explain, what outliers mean. Sometimes it is simply a matter of data (missing values), but sometimes we could find shifting alliances. Perhaps an outlier could be an MP about to switch to another party.
You can have fun with these data, too. Let us know if you discover something interesting!
Recently Orange and one of its inventors, Blaž Zupan, have been recognized as one of the top 100 changemakers in the region. A 2016 New Europe 100 is an annual list of innovators and entrepreneurs in Central and Eastern Europe highlighting novel approaches to pressing problems.
Orange has been recognized for making data more approachable, which has been our goal from the get-go. The tool is continually being developed with the end user in mind – someone who wants to analyze his/her data quickly, visually, interactively, and efficiently. We’re always thinking hard how to expose valuable information in the data, how to improve the user experience, which defaults are the most appropriate for the method, and, finally, how to intuitively teach people about data mining.
This nomination is a great validation of our efforts and it only makes us work harder. Because every research should be fruitful and fun!