text mining in biomedical research

TEXT MINING IN BIOMEDICAL RESEARCHQI LI03/28/14

REFERENCES

1. http://en.wikipedia.org/wiki/Text_mining2. D. Rebholz-Schuhmann et al., Text-mining solutions

for biomedical research: enabling integrative biology, Nature Reviews Genetics 13, 829-839 (December 2012)

3. R. King et al., The Automation of Science, Science 324, 85 (2009)

4. http://www.aber.ac.uk/~dcswww/Research/bio/robotsci/

THE USUAL WAY BIOMEDICAL RESEARCH IS DONE• Read a lot of papers on a topic• Propose one or more hypotheses• Design a series of experiments• Perform the experiments• Prove or disprove the hypotheses• Publish the results on a journal

Pic: http://www1.plymouth.ac.uk/courses/undergraduate/0732/pages/coursedetail.aspx

WHY DO WE NEED TEXT MINING• Scientists publish papers, not relations or

data instances• We need to reconstruct the knowledge out of

the publications• Then, computers will be able to help us

analyze the knowledge base, probably bringing us new ideas

OVERVIEW OF THE PROCESS

Figure: Text-mining solutions for biomedical research: enabling integrative biology [2]

SOME OF THE TECHNIQUES

Figure: Text-mining solutions for biomedical research: enabling integrative biology [2]

ONE PROTOTYPE APPLICATION: ROBOT SCIENTIST “ADAM”

Pics: http://www.aber.ac.uk/en/cs/research/cb/projects/robotscientist/pictures/

NOT JUST EXPERIMENTS: HYPOTHESES GENERATION, TOO• Gather information from a knowledge base• Propose hypotheses• Design a series of experiments• Run the experiments physically• Interpret the results• Publish the results on a journal (NOT YET)

SEE IT IN ACTION!

• http://www.aber.ac.uk/en/cs/research/cb/projects/robotscientist/video/

THANK YOU!