introduction to artificial intelligence: applications in computational biology
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Introduction to Artificial Intelligence: Applications in Computational Biology. Susan M. Bridges [email protected]. Outline. What is AI? Search Expert systems Uncertainty Machine learning Data mining. Intelligent Systems and Computational Biology. - PowerPoint PPT PresentationTRANSCRIPT
Intelligent Systems Laboratory
Introduction to Artificial Intelligence: Applications in
Computational Biology
Susan M. Bridges [email protected]
Intelligent Systems Laboratory
Outline• What is AI?
• Search
• Expert systems
• Uncertainty
• Machine learning
• Data mining
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Intelligent Systems and Computational Biology
• First applications (DNA) in which great progress was made were digital• Signal processing algorithms• Text processing techniques
• Many of the most interesting and difficult problems to be tackled are analog• Protein structure• Gene expression• Metabolic networks
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Definitions of AI(What is AI?)
• Rich, E. and K. Knight . 1991. Artificial Intelligence. New York: McGraw-Hill.
“Artificial intelligence (AI) is the study of how to make computers do things which at the moment, people do better.”
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Another definition of AI• Winston, Patrick Henry. 1984. Artificial Intelligence.
1984. Addison-Wesley, Reading, MA.
“Artificial Intelligence is the study of ideas that enable computers to be intelligent. Intelligence includes: ability to reason, ability to acquire and apply knowledge, ability to perceive and manipulate things in the physical world, and others.”
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Why Study AI?
• Understand human human intelligence
• Develop “intelligent” machines• Robotics
• Programs with intelligent properties
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Acting Rationally:Turing Test Approach
Interrogator
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AI Tasks
• Mundane tasks• Perception
» Vision
» Speech
• Natural Language» Understanding
» Generation
» Translation
• Common sense reasoning
• Robot control
• Formal tasks• Games
• Mathematics» Geometry
» Logic
» Integral calculus
• Expert tasks• Engineering
• Scientific analysis
• Medical diagnosis
• Financial analysis
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Intelligent Agents• Agent
• Perceives its environment using sensors• Acts on environment using effectors
• Rational agent • An agent that does the right thing • Basis for action
» A measure of degree of success.» Knowledge of what has been perceived so far.» The actions that the agent can perform
• Autonomous Agent• Learns from experience• Makes independent decisions
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Major Topics
• Search
• Knowledge Representation
• Machine Learning
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Problem-solving agent• A type of goal-based agent
• Find sequence of actions that lead to a desirable state
• Intelligent agents should make a set of changes in the state of the environment that maximizes the performance measure
• Life is simpler if we can set a goal and aim to satisfy it.
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Components of a problem• Initial state• Set of possible actions
• actions can be described as operators» an operator describes an action by specifying the state that can be
reached by carrying out an action in a particular state
• actions can be described in terms of a successor function S. Given a particular state x, S(x) returns the set of states reachable from x by any single action.
Operator aState x State y
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State Space• The set of all states reachable from the initial
state by any sequence of actions
• A path in the state space is a sequence of actions leading from one state to another
• The agent can apply a goal test to any single state to determine if it is a goal state.
• If one path is preferable to another, then we may need to compute path cost (g).
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5 4
7
6 1 8
3 2
1 2
7
8
3
4
6 5
Initial State Goal State
States Goal Test
Operators Path Cost
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Mathiston
PhebaWest Point
Maben
Starkville
Columbus
Ackerman
Sturgis Artesia
Crawford
BrooksvilleLouisville
Mayhew
Problem: Find route from Louisville to West Point
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LouisvilleA. The initial state
Louisville
Ackerman Starkville Brooksville
B. After expanding Louisville
C. After expanding Ackerman
Louisville
Ackerman Starkville Brooksville
Maben Sturgis Louisville
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Some terms• New states are generated from old states by
operators.
• This is called expanding the state.
• The choice of which state to expand first is called the search strategy
• Result is called a search tree
• The set of nodes waiting to be expanded is called the fringe or frontier
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Search Strategies• Requirements for a good search strategy
• causes motion
• is systematic
• State space can usually be represented as a tree or a graph
• Two important parameters of a tree• branching factor (b)
• depth (d)
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Two Types of Searches• Uninformed or blind search
• systematically generate states
• test states to see if they are goal states
• Informed or heuristic search• use knowledge about the problem domain
• explore search space more efficiently
• may sacrifice accuracy for speed
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Breadth-first search• All nodes at each depth d are expanded
before any nodes at depth d+1
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Depth-first search Always expands one of the nodes at the
deepest level of the tree Parameter m is the maximum depth
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What is a heuristic?(rule of thumb)
• A heuristic is a formalized rule for choosing those branches in a state space that are most likely to lead to an acceptable solution (Luger and Stubblefield, 1998).
• Used two ways• some problems do not have exact solutions, so we
just do the best we can (medical diagnosis)
• there may be an exact solution, but it may be very expensive to find
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Hill Climbing• Use an heuristic function (or objective or
evaluation function) to decide which direction to move in the search space.
• Always move toward the state that appears to be best (basing all decisions on local information).
• Assume that we want to maximize the value of the function.
• Can also be used for minimization (called gradient descent)
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1 2 3
7 8 4
6 5
1 2 3
7 4
6 8 5
1 2 3
7 8 4
6 6 5
1 2 3
7 8 4
6 5h=
Goal
1 2 3
8 4
7 6 5
Steepest Ascent Hill Climbing
Using Manhattan Distance
Heuristic
h= h=
1 2 3
7 8 4
7 6 5
h=
1 2 3
7 8 4
6 6 5
h=
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A* Search• Minimizing the total path cost
• Combines uniform-cost search and greedy search.
• Evaluation function:f(n) = g(n) + h(n)
g(n): cost of path from start to node n
h(n): estimate of cost of path from n to goal
f(n): estimated cost of the cheapest solution through n
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Goal: Minimum length path.
Is h(n) an admissible heuristic?
f(n) = g(n) + h(n)
K (18) L ( 3) M(2) N(9) O(5) P(2) Q(10) R(12)
S (18) T(0) U (0)
A(22)
B (18) C (21) D (8)
E(12) F(7) G (9) H(6) I (13) J(14)
d = 0
d = 1
d = 2
d = 3
d = 4
5 103
6 12 4 7 8 11
3 11 4 2 7 1 5 12 3 4
3 4 14 6 5
Numbers in parentheses are h(n)
Numbers on edges are operator costs
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Multiple Sequence Alignment • DNA and protein sequences
• Alignment of multiple sequences created by inserting gaps to shift characters to matching positions
ATCG -ATCG- TGA --T-GA
GAT GAT---
• Optimal alignment maximizes the number of matching positions
Multiple Sequence Alignment As State-Space Search
(Eric Hansen, Rong Zhou)
ATCG -ATCG- TGA --T-GA
GAT GAT---
start
goal
Space Complexity: O (LN) Time Complexity: O (2NLN)Where L is the average length of sequences and N is the number of sequences
Nodes pruned by Anytime A*
An Illustration of Anytime A*
0 918
5 617
4 718
7 415
8 314
9 213
3 716
2 818
11 011
1 919
6 516
4 718
3 819
2 920
g hf
f = g + 2h
Goal
g hf
= expanded node
g hf= stored but not
expanded node
Total number of nodes stored = 8
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Genetic Algorithms• Search procedure based on a simple model
of evolution
• Uses a “random” process to explore search space
• Has been applied in many domains
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Terminology• Begin with a population of individuals. Each individual
represents a solution to the problem we are trying to solve.
• A data structure describes the genetic structure of the individual. (Assume for initial discussion that this is a string of 0’s and 1’s).
• In genetics, the strings are called chromosomes and the bits are called genes.
• The string associated with each individual is its genotype
• Selection is based on fitness of individuals
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The Genetic Algorithm• Each evolving population of individuals is
called a generation.
• Given a population of individuals corresponding to one generation, the algorithm simulates natural selection and reproduction in order to obtain the next generation.
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Three basic operations• Reproduction:
• Individuals from one generation are selected for the next generation
• Crossover: • Genetic material from one individual is exchanged
with genetic material from another individual
• Mutation: • Genetic material is altered
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General GA ProcedureSelection, crossover, and mutation operations
Initial population
Parent candidate pool Father and
Mother
Offspring
Crossover and mutate
Next generation populationConverge?
Evaluate fitness
Evaluate fitness and replace
Select parents
no
yes
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Example of General GA Procedure
Selection, crossover, and mutation operations
Generation n 1 1 0
11 0 1
10 1 0
01 0 0
1
11 13 2 9
Reproduction 1 1 0
11 0 1
11 0 0
11 0 1
1Crossover
1 1 1 0 1
0 1 1
Mutation
1 0 0 1
1 0
0 1
1 1
1
0 1 1
1 0 1
0
1 0 1 1
0 0
1 0 0 1
1 1
Generation n+ 1
15 8 1 13
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Two keys to the success of a GA
• Data structures for»Genes»Chromosomes»Population
• Fitness evaluation function
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Knowledge Representation
• Semantic networks
• Frame based systems
• Rule based expert systems
• Ontologies
• Neural networks
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Anything
AbstractObjects Events
Sets NumbersRepresentational
Objects
Intervals
Places
PhysicalObjects
Processes
Categories
Sentences Measurements
Moments
Times Weights
Things Stuff
Animals Agents
Humans
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Expert Systems
• Rule based systems• Garnered a great deal of attention in the 1980’s
• Most famous examples are in medical domains
• Stimulated interest in “logic programming”
• Encode knowledge of people as sets of rules
• Still widely used
• Knowledge acquisition bottleneck
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Representing Uncertainty
• Fuzzy logic
• Bayesian reasoning
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Uncertainty versus Vagueness• Certainty–degree of belief
• there is a 50% probability of rain today
• I am 30 % sure the patient is suffering from pneumonia
• Vagueness–the degree to which an item belongs to a category• the man is tall
• move the wheel slightly to the left
• the patient’s lungs are highly congested
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Fuzzy Sets Represent Vagueness
• Lotfi Zadeh popularized the idea in the 60’s
• Popular concept in Eastern philosophy
• Reasoning with fuzzy sets is called fuzzy logic
• Fuzzy logic is also called • approximate reasoning
• continuous logic
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Fuzzy Set Definitions• Set membership can be expressed using a
characteristic (or descrimination) function
• Classic (or crisp) setsIf objects x are chosen from some universe X
• Fuzzy sets - an element can be a partial member of a set (grade of membership)
Aset ofelement an not is x if 0
Aset ofelement an is x if 1)(xA
0 A(x) 1
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Examples of Fuzzy Concepts from Natural Language
• John is tall
• The weather is rainy
• Turn the volume up a little
• Dr. Bridges’ tests are long
• Add water until the dough is the right consistency
• There was very little change in the cost
• The water bill was somewhat high
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Representing Fuzzy Sets• Enumeration of membership values of all
elements with non-zero membership
TALL = {.125/5.5, .5/6, .875/6.5, 1/7, 1/7.5, 1/8}
• Represent membership with a function
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Functional Representations Fuzzy Set Tall
0
1
4 5 6 7
Tall
Height in feet
Membership
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Linguistic (or Fuzzy)Variable• Usually corresponds to a noun
• The values of a linguistic variable are fuzzy sets (which correspond to adjectives)
• Examples:Linguistic variable Fuzzy sets
Height short medium tall
Weight light average heavy
Temperature cold cool typical warm hot
Speed slow medium fast
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Linguistic Variable Temperature
30 40 50 60 70 80 90 100
0
1
Cold Normal Hot
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Some Fuzzy Set Operations• Set union A B
A B(x)max(A(x),B(x)) for all x X
alternate syntax (join operator)
A B(x)A(x)B(x)) for all x X
• Set intersection A BAB(x)min(A(x),B(x)) for all x X
alternate syntax (meet operator)
A B(x)A(x) B(x)) for all x X
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Fuzzy Reasoning• A fuzzy proposition is a statement that asserts a
value for a linguistic (or fuzzy) variable• Example: Joe’s height is medium
» Linguistic variable (noun) Joe’s height
» Fuzzy set (adjective) medium
» The fuzzy set “medium” is a value of the linguistic variable “Joe’s height”
• A fuzzy rule relates two or more fuzzy propositions
• Fuzzy inference techniques are used to draw conclusions using fuzzy rules
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Example Fuzzy Rule
If speed is normal
then braking.force is medium
Speed
Normal = (0/0, .1/20, .8/40, 1/60, .1/80, 0/100)
braking.force
Medium = (0/0, .5/1, 1/2, 1/3, .2/4, 0/5)
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J. Dickerson, D. Bedeant, Z.Cox, W. Qi, D. Ashlock, and E. Wurtele, Atlantic Symposium on Computational Biology and Genome Information Systems & Technology (CBGIST 2000,
26-30.
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Bayesian Reasoning• Bayesian networks: Represent knowledge as
a network of random variables
• Many names and many variations• Belief networks
• Probabilistic networks
• Causal networks
• Knowledge Maps
• Influence Diagram (extension)
• Decision Network (extension)
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Belief Network
Burglary Earthquake
Alarm
JohnCallsMaryCalls
P(B)
0.001P(E)
0.002
B E P(A|B,E) T T 0.95 T F 0.94 F T 0.29 F F 0.01
A P(J|A)
T 0.90
F 0.05
A P(M|A)
T 0.70
F 0.01
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Classification of Learning Systems
• Supervised learning• Give the system a set of examples and an
“answer” for each example.• Train the system until it can give the correct
response to these examples (or most of them).
• Unsupervised learning• Give the system a set of examples and let it
discover interesting patterns in the examples.
• Reinforcement learning• Learn from rewards and penalties
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Feature Vectors• Simple representation
used by most learning systems.
• Represents each example as a vector or numbers • Quantities
• Nominal data
• Ordinal data#53 5.3 cold 3.2 blue 1
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Neural Networks• Computational models “loosely” based on the
structure of the brain• Characteristics of the brain
• Large number of simple processing units (neurons)• Highly connected• No central control• Neurons are slow devices compared to digital computers• Can perform complex tasks in a short period of time• Neurons are failure-prone devices• Handles fuzzy situations very well.• Information accessed on the basis of content• Learns from experience
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Neural Networks• Based on model of nervous system
• Large numbers of simple processing units
• Units are highly connected and connections are weighted.
• Highly parallel distributed control
• Emphasis on learning internal representations automatically
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Neural Network Concepts• Cell or unit or neuron or node
• Autonomous processing unit that models a neuron• Purpose
» Receives information from other cells» Performs simple processing» Sends results on to one or more cells
• Layers • A collection of cells that perform a common function• Types:
» Input layer» Hidden layer» Output layer
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Layers of Neurons
I1
I2
I3
H1
H2
O1
Input Layer Hidden Layer Output Layer
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Properties• In general, there is no interconnection
between cells in the same layer
• Connections are one or two way communications links between two cells
• Weights are the strength of the connections. A weight wij is a real number than indicates the influence that cell ui has on cell uj
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More about weights• Positive weights indicate reinforcement
• Negative weights indicate inhibition
• Weight of 0 indicates no influence or connection
• Weights may be initialized to one of these:• 0
• predefined values
• random values
• Weights are altered by experience
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Multilayer Feed-Forward Networks
• Networks that are connected acyclic graphs
• Backpropagation• Most popular training method for feed forward layered
networks.
• Invented in 1969 by Bryson and Ho
• Ignored until 80’s
• Supervised learning technique
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Back Propagation• Initialize the network with random weights
• Show it an input instance
• Compute the output
• Determine how much the output differs from the goal.
• Feed small adjustments to the weights back through the network based on the error.
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General Algorithm for Training Network
Initialize NN
for epoch = 1 to MAXEPOCHS
for each input-output pair in the training set
present an example and compute error
adjust weights to reduce the error
compute mean-square-error for training set
for each input-output pair in the test set
compute error
compute mean-square-error for test set
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Generalization
% correct
Training time (# of epochs)
Training set
Test set
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Computational Biology Applications• Protein classification
• Sequence analysis
• DNA fragment assembly
• Prediction of transmembrane regions
• Phylogenetic classification of ribosome sequences
• And many more
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Self-Organizing Maps• Also called Kohonen maps
• Used for unsupervised learning
• Widely applied for comparison of gene expression data
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Principle of Self-Organizing Maps
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Self-Organizing Map from Yeast Gene Expression Data
(German Florez)
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Knowledge Discovery• Definition: Non-trivial extraction of implicit,
previously unknown, and potentially useful information from data.
• Applications in biology• Text mining
• Association rule mining
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KDD Process
Data
Target Data
--- --- --- ------ --- --- ---
PreprocessedData
TransformedData
Patterns
Knowledge
Selection
Preprocessing
Transformation
Data Mining
Interpretation/Evaluation
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Iterative Clustering Procedure( Wan, Bridges, J.Boyle, A.Boyle)
Download data from Genbank
Represent data using an appropriate method
Construct feature vector for each gene from POSITIONAL WEIGHT MATRICES
Cluster with K-clustering
Visualize results
Conclusions
Select clustering without clear patterns for further clustering
Positional Weight Matrix Representation
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S. solfataricus with A, G box (2976)Clustering window (-48 to -1)
Nearby with A, G box (286)Cluster window (-24 to -1)
With A box (1656)
With A box (146)
With G box (1320)
With A and G box (142)
Distant with A box (1370)
Nearby with G box (571)
Distant with G box (749)
Clustering Results