MODULE 5
Data Mining
• Data mining is one stage in an overall knowledge-discovery process.
Knowledge-discovery process involves:
1. Selection and sampling of the appropriate data from the database(s)
2. Preprocessing and cleaning of the data to remove redundancies, errors,
and conflicts
3. Transforming and reducing data to a format more suitable for the data
mining
4. Data mining
5. Evaluation of the mined data
6. Visualization of the evaluation results
7. Designing new data queries to test new hypotheses and returning to step
1
1. Selection and Sampling
• In a large database or data warehouse, there may be hundreds
or thousands of valueless relationships.
• identify potentially valuable relationships.
2. Preprocessing and Cleaning.
preparing the data for the actual analysis associated with data mining
Data Mining Preparatory Activities
Data Characterization :-creating a high-level description of the nature and the content
of the data to be mined
Consistency Analysis:-a statistical assessment of data, based solely on data values.
Domain Analysis :-verifying that a data value is a text string or an integer, or that it's
statistically consistent with other data on the same parameter, to ensure that it
makes sense in the context of the biology
Data Enrichment :-drawing from multiple data sources to minimize the limitations of a
single data source.
Frequency and Distribution Analysis :-places weights on values as a function of their
frequency of occurrence.
Normalization :-transforming data values from one representation to another, using a
predefined range of final values.
3. Transformation and Reduction
• The transformation and reduction phase of the knowledge-
discovery process, data sets are reduced to the minimum size
possible through sampling or summary statistics.
• Transformation involves translating one type of data to
another through mathematical or mapping operations.
4. Data-Mining Methods.
• The process of data mining is concerned with extracting
patterns from the data, typically using classification,
regression, link analysis, segmentation, or deviation detection.
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• The patterns identified by the data-mining analysis are
interpreted.
6. Visualization
• Visualization can range from converting tabular listings of
data summaries to pie charts and similar business graphics.
Pattern Recognition and Discovery
• Data mining involves pattern recognition and pattern
discovery.
• In bioinformatics, pattern recognition is most often concerned
with the automatic classification of character sequence.
• The pattern-recognition process starts with an unknown
pattern, such as a potential protein structure, and ends with a
label for the pattern.
• The major steps in the pattern recognition and discovery
process are:
1. Feature Selection:-
• Given a pattern, the first step in pattern recognition is to
select a set of features or attributes from the universe of
available features that will be used to classify the pattern.
• When pattern recognition is directed at known patterns, the
researcher defines a priori the features that will be used to
distinguish the pattern from other data.
2. Measurement.
• Involves converting the original pattern into a representation
that can be easily manipulated programmatically.
• For example, a 3D vector image of a protein might be
represented as a series of 2D matrices.
• Similarly, a nucleotide sequence may be represented by a
series of integers (for example, A = 1, T = 2, C = 3, and G =
4), depending on the underlying technology used to perform
the pattern-matching operation.
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• After the measurement process, the data are processed to
remove noise and prepare for feature extraction.
• Processing typically involves executing a variety of error
checking and correction routines, as well as specialized
processes that depend on the nature of the data.
• For example, images may undergo edge enhancement and
transformation to correct for size and orientation variations
(normalization) in order to facilitate feature extraction.
4. Feature Extraction.
• Involves searching for global and local features in the
data that are defined as relevant to pattern matching
during feature selection.
• Clustering techniques, in which similar data are
grouped together, often form the basis of feature
extraction.
5. Classification and Discovery.
• In the classification phase of pattern recognition and
discovery, data are classified based on measurements of
similarity with other patterns.
6. Labeling
• The pattern-recognition process ends when a label is assigned
to the data, based on its membership in a class.
Machine Learning
1. Inductive Logic Programming
• uses a set of rules or heuristics to categorize data.
• A common rule is to use change in entropy to iteratively
choose an attribute of the data that will subset the data
according to the attribute.
• That is, an entropy-based classification system based on
an induction algorithm works by incrementally dividing
the data into the largest possible spaces until all data has
been assigned to a collection.
2. Genetic Algorithm
• Based on evolutionary principles wherein a particular
function or definition that best fits the constraints of an
environment survives to the next generation, and the
other functions are eliminated.
• Evaluate a large number of solutions to a problem that
are generated at random.
• The members of the solution population with the
highest fitness scores are allowed to "mate" with
crossovers and mutations, creating the next generation.
3. Neural Network
4. Decision Trees
5. Hidden Markov Model(HMM)
• A Hidden Markov Model (HMM) is a statistical model for an
ordered sequence of symbols, acting as a stochastic state
machine that generates a symbol each time a transition is
made from one state to the next.
• Transitions between states are specified by transition
probabilities.
• A Markov process is a process that moves from state to state
depending on the previous n states.
• The process is called an order n model where n is the number
of states affecting the choice of the next state.
• The Markov process considered here is a first order, in that the
probability of a state is dependent only on the directly
• Consider the concept of a Markov Chain, which is a process
that can be in one of a number of states at any given time.
• Each state generates an observation, from which the state
sequence can be inferred.
• Markov Chain is defined by the probabilities for each
transition in state occurring, given the current state. That is, a
Markov Chain is a non-deterministic system in which it is
assumed that the probability of moving from one state to
another doesn't vary with time.
• A HMM is a variation of a Markov Chain in which the states
in the chain are hidden.
• Like a neural network classifier, a HMM must be trained
before it can be used.
• Training establishes the transition probabilities for each state
in the Markov Chain.
• When presented with data in the database, the HMM provides
a measure of how close the data patterns—sequence data, for
example—resemble the data used to train the model.