Former ACM President David Patterson on Using Software to Target Sources of Cancer
February 4, 2016
ACM Fellow and former ACM President David Patterson has been a computer science professor at the University of California, Berkeley for nearly four decades. Known for his contributions to RISC and RAID computer architectures, he was instrumental in the founding of UC Berkeley's Algorithms, Machines and People (AMPLab), which explores the role big data may play in finding a cure for cancer and other diseases.
Patterson's blog post, the latest contribution in an ongoing series on current issues in technology and society by ACM leaders and members for The Huffington Post, describes how the AMPLab, in collaboration with Microsoft Research and UC Santa Cruz, developed software that helped save a life. Through genetic sequencing and analysis, a rare pathogen was identified, allowing identification of a rare contagious bacterium that was causing seizures in a patient. "Our program first filtered out the human portion of the DNA data, which was 99.98% of the original 3 million pieces of data, and then sequenced the remaining pathogen," says Patterson. "Although our software is only part of this process, previously doctors had to guess the causative agent before testing for a contagious disease. Other hospitals and the Centers for Disease Control now use this procedure."
Ultimately, says Paterson, we need funding to advance the expansion of genetic repositories for study, as well as policies that will enable secure sharing of genomic and clinical data. "We need to
draft software experts immediately who can leverage advances in cloud computing and machine learning while protecting patient privacy to start building open-source tools that will enable scientists
to make major inroads on cancer."
Read his People of ACM interview.