Protein classification and the k-Nearest Neighbors algorithm
by Richard Heimann, Nathan Danneman, Pradeepta Mishra, Bater Makhabel
R: Mining Spatial, Text, Web, and Social Media Data
- R: Mining Spatial, Text, Web, and Social Media Data
- Table of Contents
- R: Mining Spatial, Text, Web, and Social Media Data
- R: Mining Spatial, Text, Web, and Social Media Data
- Credits
- Preface
- 1. Module 1
- 1. Warming Up
- 2. Mining Frequent Patterns, Associations, and Correlations
- An overview of associations and patterns
- Market basket analysis
- Hybrid association rules mining
- Mining sequence dataset
- The R implementation
- High-performance algorithms
- Time for action
- Summary
- 3. Classification
- Classification
- Generic decision tree induction
- High-value credit card customers classification using ID3
- Web spam detection using C4.5
- Web key resource page judgment using CART
- Trojan traffic identification method and Bayes classification
- Identify spam e-mail and Naïve Bayes classification
- Rule-based classification of player types in computer games and rule-based classification
- Time for action
- Summary
- 4. Advanced Classification
- 5. Cluster Analysis
- 6. Advanced Cluster Analysis
- Customer categorization analysis of e-commerce and DBSCAN
- Clustering web pages and OPTICS
- Visitor analysis in the browser cache and DENCLUE
- Recommendation system and STING
- Web sentiment analysis and CLIQUE
- Opinion mining and WAVE clustering
- User search intent and the EM algorithm
- Customer purchase data analysis and clustering high-dimensional data
- SNS and clustering graph and network data
- Time for action
- Summary
- 7. Outlier Detection
- Credit card fraud detection and statistical methods
- Activity monitoring – the detection of fraud involving mobile phones and proximity-based methods
- Intrusion detection and density-based methods
- Intrusion detection and clustering-based methods
- Monitoring the performance of the web server and classification-based methods
- Detecting novelty in text, topic detection, and mining contextual outliers
- Collective outliers on spatial data
- Outlier detection in high-dimensional data
- Time for action
- Summary
- 8. Mining Stream, Time-series, and Sequence Data
- 9. Graph Mining and Network Analysis
- 10. Mining Text and Web Data
- A. Algorithms and Data Structures
- 2. Module 2
- 1. Data Manipulation Using In-built R Data
- What is data mining?
- Introduction to the R programming language
- Data type conversion
- Sorting and merging dataframes
- Indexing or subsetting dataframes
- Date and time formatting
- Creating new functions
- Loop concepts - the for loop
- Loop concepts - the repeat loop
- Loop concepts - while conditions
- Apply concepts
- String manipulation
- NA and missing value management
- Missing value imputation techniques
- Summary
- 2. Exploratory Data Analysis with Automobile Data
- Univariate data analysis
- Bivariate analysis
- Multivariate analysis
- Understanding distributions and transformation
- Interpreting distributions
- Variable binning or discretizing continuous data
- Contingency tables, bivariate statistics, and checking for data normality
- Hypothesis testing
- Non-parametric methods
- Summary
- 3. Visualize Diamond Dataset
- 4. Regression with Automobile Data
- 5. Market Basket Analysis with Groceries Data
- 6. Clustering with E-commerce Data
- 7. Building a Retail Recommendation Engine
- 8. Dimensionality Reduction
- 9. Applying Neural Network to Healthcare Data
- 1. Data Manipulation Using In-built R Data
- 3. Module 3
- 1. Going Viral
- 2. Getting Started with R
- 3. Mining Twitter with R
- 4. Potentials and Pitfalls of Social Media Data
- 5. Social Media Mining – Fundamentals
- Key concepts of social media mining
- Good data versus bad data
- Understanding sentiments
- Sentiment polarity – data and classification
- Supervised social media mining – lexicon-based sentiment
- Supervised social media mining – Naive Bayes classifiers
- Unsupervised social media mining – Item Response Theory for text scaling
- Summary
- 6. Social Media Mining – Case Studies
- A. Conclusions and Next Steps
- Bibliography
- Index
The k-Nearest Neighbors (kNN) algorithm is one of the lazy learners that postpones the learning until the test tuple or test instance is provided.
A single training tuple is represented by a point in an n-dimensional space. In other words, n attributes' combinations are used to represent the specific training tuple. There is no specific training before the arrival of the test tuple that needs to be classified. Some preprocessing steps are needed, such as normalization for some attributes with large values compared to other attributes' values. Data normalization approaches in the data transformation can be applied here for preprocessing.
When a test tuple is given, the k-nearest training tuples are found from the training tuples space by a specific measure to calculate the distance between test tuple and the training tuple. The k-nearest training tuples are also known as the kNN. One popular solution is the Euclidean distance in real space, illustrated in the following equation. This method is only applicable to numeric attributes:
For nominal attributes, one solution is that the difference between two attribute values is defined as 1, or as 0. We already know that many approaches deal with missing values in the attributes. With a predefined threshold, the value of k is selected with the number of tuples with the lowest error-rate among all the training tuples.
The class label of the test tuple is defined by the voting of the most common class in the kNN.
The input parameters for kNN algorithm are as follows:
- D, the set of training objects
- z, the test object, which is a vector of attribute values
- L, the set of classes used to label the objects
The output of the algorithm is the class of z, represented as 
.
The pseudocode snippet for kNN is illustrated here:
The I function in line 6 denotes an indicator function that returns the value 1 if its argument is true and 0 otherwise.
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