Detecting Salient Changes in Gene Profiles
Detecting Salient Changes in Gene Profiles
Sohei Okamoto University of Nevada, Reno
Dr. Tanveer Syeda-Mahmood IBM Almaden Research Center
Dr. George Bebis University of Nevada, Reno
Dr. Dwight Egbert University of Nevada, Reno
Sohei Okamoto University of Nevada, Reno
Dr. Tanveer Syeda-Mahmood IBM Almaden Research Center
Dr. George Bebis University of Nevada, Reno
Dr. Dwight Egbert University of Nevada, Reno
OUTLINEOUTLINE
• Motivation
• Approach
• Method
• Difficulty
• Future Work
• Motivation
• Approach
• Method
• Difficulty
• Future Work
MOTIVATIONMOTIVATION
• Salient changes in gene expressions indicate important events such as onset of disease.
• Salient changes in multiple gene profiles are similarities among them
• Salient changes in gene expressions indicate important events such as onset of disease.
• Salient changes in multiple gene profiles are similarities among them
• Salient changes are maxima in vector magnitude function
• Build scale-space bitmap, and find salient change contours
• Choose optimal smoothing scale by objective functions
• Salient changes are maxima in vector magnitude function
• Build scale-space bitmap, and find salient change contours
• Choose optimal smoothing scale by objective functions
APPROACHAPPROACH
• Finding maxima in vector magnitude function
• Salient change is inflection point which has maximum slope
• Finding maxima in vector magnitude function
• Salient change is inflection point which has maximum slope
METHOD – Salient ChangesMETHOD – Salient Changes
Maxima and minima of derivative
Maxima and minima of derivative
Maxima of vector magnitude
Maxima of vector magnitude
Points obtained in input signalPoints obtained in input signal
METHOD – Salient ChangesMETHOD – Salient Changes
METHOD – Scale-SpaceMETHOD – Scale-Space
• Scale-space visualizes how salient changes preserved over increasing scale of smoothing
• Gaussian smoothing with increasing standard deviation
• Scale-space visualizes how salient changes preserved over increasing scale of smoothing
• Gaussian smoothing with increasing standard deviation
METHOD – Scale-SpaceMETHOD – Scale-Space
Result of increasing smoothingResult of increasing smoothing
METHOD – Scale-SpaceMETHOD – Scale-Space
Input signalInput signal
Vector magnitudeVector magnitude
Derivative of vector magnitude
Derivative of vector magnitude
METHOD – Scale-SpaceMETHOD – Scale-Space
• Construct binary representation of vector magnitude derivative for each increasing scale
• Construct binary representation of vector magnitude derivative for each increasing scale
METHOD – Scale-SpaceMETHOD – Scale-Space
• Negative-going zero-crossing contours in scale-space
• Negative-going zero-crossing contours in scale-space
METHOD – Optimal Scale SelectionMETHOD – Optimal Scale Selection
• Select optimal smoothing scale to ignore non-significant salient change with minimum error
• Calculate objective functions and combine
• Select optimal smoothing scale to ignore non-significant salient change with minimum error
• Calculate objective functions and combine
METHOD – Optimal Scale SelectionMETHOD – Optimal Scale Selection
• Roughness – # of salient changes at each scale
• Mean Square Error – Error between input and smoothed signal at each scale:
• Combined objective function – take average of two functions
• Roughness – # of salient changes at each scale
• Mean Square Error – Error between input and smoothed signal at each scale:
• Combined objective function – take average of two functions
METHOD – Optimal Scale SelectionMETHOD – Optimal Scale Selection
• Find crossing point of two objective functions, which is also minimum of combined objective function
• Find crossing point of two objective functions, which is also minimum of combined objective function
METHOD – Optimal Scale SelectionMETHOD – Optimal Scale Selection
• Trace back salient change contours exist at optimal scale to lowest scale
• Trace back salient change contours exist at optimal scale to lowest scale
METHOD – Optimal Scale SelectionMETHOD – Optimal Scale Selection
• Salient changes found• Salient changes found
DIFFICULTYDIFFICULTY
• When there are relatively few salient change contours
• When there are relatively few salient change contours
DIFFICULTYDIFFICULTY
• when one contour branch out to two at some lower scale
• when one contour branch out to two at some lower scale
DIFFICULTYDIFFICULTY
• When time points are few
• Visualization of more than 3-dimensional signal
• When time points are few
• Visualization of more than 3-dimensional signal
FUTURE WORKFUTURE WORK
• Collect large amount of results using this method for validity
• Adding analysis functionality as an event mining tool
• Integration with other data mining tools
• Collect large amount of results using this method for validity
• Adding analysis functionality as an event mining tool
• Integration with other data mining tools
ACKNOWLEDGMENTACKNOWLEDGMENT
• University of Nevada, Reno, Computer Science Department
• UNR, Computer Vision Laboratory
• UNR-CRCD Program in Computer Vision
• IBM Almaden Research Center
• National Science Foundation
• University of Nevada, Reno, Computer Science Department
• UNR, Computer Vision Laboratory
• UNR-CRCD Program in Computer Vision
• IBM Almaden Research Center
• National Science Foundation