DEC 03, 2019 01:41 PM PST

Using deep learning to find the patterns of cancer

Research published recently in the journal Life Science Alliance uses deep learning to analyze genomic data from colorectal tumors to ameliorate diagnosis accuracy. Because colorectal tumors come in so many different forms, accurately diagnosing them can be a challenge; this can then impact the accuracy of subsequent information provided to patients regarding survival rates and treatment options. The recent research was conducted by scientists at the Max Delbrück Center for Molecular Medicine in the Helmholtz Association.

"Disease is much more complex than just one gene," explains Altuna Akalin, bioinformatics scientist who leads the Bioinformatics Platform research group at MDC's Berlin Institute of Medical Systems Biology (BIMSB). "To appreciate the complexity, we have to use some kind of machine learning to really make use of all the data."

The machine learning that Akalin and first author Jonathan Ronen designed to handle the complexity of gene expression is called the Multi-omics Autoencoder Integration platform, nicknamed "maui". Maui is capable of analyzing genetic material, gene expression, single point mutations and DNA copy-numbers in order to identify gene sets or pathways that lead to colorectal cancer.

In testing maui, the researchers found that it was correctly able to identify patterns that we already know to be related to the four subtypes of colorectal cancer. This verifies the system’s ability to manage large amounts of information. "Data science can handle complex data that is hard to handle other ways and makes sense of it," Akalin explained. "You can feed it everything you have on the tumors and it finds meaningful patterns."

Maui was also able to discern 100 patterns within three minutes – a fraction of the time that similar systems require. Additionally, maui was more accurate than other systems. "It is able to learn orders of magnitude more latent factors, at a fraction of the computation time," commented Ronen.

Akalin and Ronen say that this deep learning platform could be used to detect and categorize cancerous colorectal tumors, as well as help improve predictions on responses to certain treatments. "Think of this like a search engine," Akalin exclaimed. That is, of course, after it has been approved in clinical trials, which is still some ways in off. However, once it arrives, the researchers say there is potential to modify maui to be used with other kinds of cancer in addition to colorectal tumors.

Sources: Life Science Alliance, Science Daily

About the Author
  • Kathryn is a curious world-traveller interested in the intersection between nature, culture, history, and people. She has worked for environmental education non-profits and is a Spanish/English interpreter.
You May Also Like
DEC 14, 2019
Cancer
DEC 14, 2019
Looking at the bigger picture: immune cells in a human body
While laboratory-conducted research has allowed for countless scientific advancements over the years, it may not come as a surprise that studying cells in ...
DEC 14, 2019
Genetics & Genomics
DEC 14, 2019
Membrane-less Organelle Found to Play a Role in Preventing Cancer
In recent years, scientists have found that a phenomenon called phase separation plays a critical role in the functions of cells....
DEC 14, 2019
Cancer
DEC 14, 2019
Specific gut bacteria linked to bowel cancer
New research suggests that the presence of a certain kind of gut bacteria can increase the risk of bowel cancer by as much as 15%. The research is importan...
DEC 14, 2019
Cancer
DEC 14, 2019
Understanding H. pylori and gastric cancer
New research published in the journal Gastroenterology offers insight on gastric cancer and the presence of the common bacteria known as H. pylori (Helicob...
DEC 14, 2019
Cancer
DEC 14, 2019
When the numbers don't match: inaccuracy in late state breast cancer survival estimates
According to the World Health Organization, about 2.1 million women are diagnosed with breast cancer annually. It is the cancer that most affects women and...
DEC 14, 2019
Genetics & Genomics
DEC 14, 2019
Mining 'Junk' DNA for New Cancer Therapeutics
There are vast portions of the genome that don't code for protein, but researchers are learning more about how important they are....
Loading Comments...