OmicsFootPrint: Mayo Clinic's AI Tool Offers a New Way to Visualize Disease

Mayo Clinic researchers have pioneered an artificial intelligence (AI) tool, called OmicsFootPrint, that helps convert vast amounts of complex biological data into two-dimensional circular images. The details of the tool are published in a study in Nucleic Acids Research.

Omics is the study of genes, proteins and other molecular data to help uncover how the body functions and how diseases develop. By mapping this data, the OmicsFootPrint may provide clinicians and researchers with a new way to visualize patterns in diseases, such as cancer and neurological disorders, that can help guide personalized therapies. It may also provide an intuitive way to explore disease mechanisms and interactions.

"Data becomes most powerful when you can see the story it's telling," says lead author Krishna Rani Kalari, Ph.D., associate professor of biomedical informatics at Mayo Clinic's Center for Individualized Medicine. "The OmicsFootPrint could open doors to discoveries we haven't been able to achieve before."

Genes act as the body’s instruction manual, while proteins carry out those instructions to keep cells functioning. Sometimes, changes in these instructions - called mutations - can disrupt this process and lead to disease. The OmicsFootPrint helps make sense of these complexities by turning data - such as gene activity, mutations and protein levels - into colorful, circular maps that offer a clearer picture of what’s happening in the body.

In their study, the researchers used the OmicsFootPrint to analyze drug response and cancer multi-omics data. The tool distinguished between two types of breast cancer - lobular and ductal carcinomas - with an average accuracy of 87%. When applied to lung cancer, it demonstrated over 95% accuracy in identifying two types: adenocarcinoma and squamous cell carcinoma.

The study showed that combining several types of molecular data produces more accurate results than using just one type of data.

The OmicsFootPrint also shows potential in providing meaningful results even with limited datasets. It uses advanced AI methods that learn from existing data and apply that knowledge to new scenarios - a process known as transfer learning. In one example, it helped researchers achieve over 95% accuracy in identifying lung cancer subtypes using less than 20% of the typical data volume.

"This approach could be beneficial for research even with small sample size or clinical studies," Dr. Kalari says.

To enhance its accuracy and insights, the OmicsFootPrint framework also uses an advanced method called SHAP (SHapley Additive exPlanations). SHAP highlights the most important markers, genes or proteins that influence the results to help researchers understand the factors driving disease patterns.

Beyond research, the OmicsFootPrint is designed for clinical use. It compresses large biological datasets into compact images that require just 2% of the original storage space. This could make the images easy to integrate into electronic medical records to guide patient care in the future.

The research team plans to expand the OmicsFootPrint to study other diseases, including neurological diseases and other complex disorders. They are also working on updates to make the tool even more accurate and flexible, including the ability to find new disease markers and drug targets.

Tang X, Prodduturi N, Thompson KJ, Weinshilboum R, O'Sullivan CC, Boughey JC, Tizhoosh HR, Klee EW, Wang L, Goetz MP, Suman V, Kalari KR.
OmicsFootPrint: a framework to integrate and interpret multi-omics data using circular images and deep neural networks.
Nucleic Acids Res. 2024 Nov 27;52(21):e99. doi: 10.1093/nar/gkae915

Most Popular Now

Relationship Between Sleep and Nutrition…

Diet and sleep, which are essential for human survival, are interrelated. However, recently, various services and mobile applications have been introduced for the self-management of health, allowing users to record...

AI Model can Read ECGs to Identify Femal…

A new AI model can flag female patients who are at higher risk of heart disease based on an electrocardiogram (ECG). The researchers say the algorithm, designed specifically for female patients...

New AI Tool Mimics Radiologist Gaze to R…

Artificial intelligence (AI) can scan a chest X-ray and diagnose if an abnormality is fluid in the lungs, an enlarged heart or cancer. But being right is not enough, said...

To be Happier, Take a Vacation... from Y…

Today, nearly every American - 91% - owns a cellphone that can access the internet, according to the Pew Research Center. In 2011, only about one-third did. Another study finds...

Researchers Find Telemedicine may Help R…

Low-value care - medical tests and procedures that provide little to no benefit to patients - contributes to excess medical spending and both direct and cascading harms to patients. A...

AI Revolutionizes Glaucoma Care

Imagine walking into a supermarket, train station, or shopping mall and having your eyes screened for glaucoma within seconds - no appointment needed. With the AI-based Glaucoma Screening (AI-GS) network...

North Cumbria Integrated Care Signs 10-Y…

North Cumbria Integrated Care NHS Foundation Trust (NCIC) has signed a long-term agreement for use of the Alcidion Miya Precision platform, to provide an electronic patient record (EPR) for the...

AI Accelerates Discovery of Neurodevelop…

Researchers have developed an artificial intelligence (AI) approach that accelerates the identification of genes that contribute to neurodevelopmental conditions such as autism spectrum disorder, epilepsy and developmental delay. This new...

AI may Help Clinicians Personalize Treat…

Individuals with generalized anxiety disorder (GAD), a condition characterized by daily excessive worry lasting at least six months, have a high relapse rate even after receiving treatment. Artificial intelligence (AI)...

AI can Open Up Beds in the ICU

At the height of the COVID-19 pandemic, hospitals frequently ran short of beds in intensive care units. But even earlier, ICUs faced challenges in keeping beds available. With an aging...

AI Model Predicting Two-Year Risk of Com…

AFib (short for atrial fibrillation), a common heart rhythm disorder in adults, can have disastrous consequences including life-threatening blood clots and stroke if left undetected or untreated. A new study...

New Research Explores How AI can Build T…

In today’s economy, many workers have transitioned from manual labor toward knowledge work, a move driven primarily by technological advances, and workers in this domain face challenges around managing non-routine...