AI researchers ask: What's going on inside the black box?

February 08, 2021

Cold Spring Harbor Laboratory (CSHL) Assistant Professor Peter Koo and collaborator Matt Ploenzke reported a way to train machines to predict the function of DNA sequences. They used "neural nets", a type of artificial intelligence (AI) typically used to classify images. Teaching the neural net to predict the function of short stretches of DNA allowed it to work up to deciphering larger patterns. The researchers hope to analyze more complex DNA sequences that regulate gene activity critical to development and disease.

Machine-learning researchers can train a brain-like "neural net" computer to recognize objects, such as cats or airplanes, by showing it many images of each. Testing the success of training requires showing the machine a new picture of a cat or an airplane and seeing if it classifies it correctly. But, when researchers apply this technology to analyzing DNA patterns, they have a problem. Humans can't recognize the patterns, so they may not be able to tell if the computer identifies the right thing. Neural nets learn and make decisions independently of their human programmers. Researchers refer to this hidden process as a "black box". It is hard to trust the machine's outputs if we don't know what is happening in the box.

Koo and his team fed DNA (genomic) sequences into a specific kind of neural network called a convolutional neural network (CNN), which resembles how animal brains process images. Koo says:

"It can be quite easy to interpret these neural networks because they'll just point to, let's say, whiskers of a cat. And so that's why it's a cat versus an airplane. In genomics, it's not so straightforward because genomic sequences aren't in a form where humans really understand any of the patterns that these neural networks point to."

Koo's research, reported in the journal Nature Machine Intelligence, introduced a new method to teach important DNA patterns to one layer of his CNN. This allowed his neural network to build on the data to identify more complex patterns. Koo's discovery makes it possible to peek inside the black box and identify some key features that lead to the computer's decision-making process.

But Koo has a larger purpose in mind for the field of artificial intelligence. There are two ways to improve a neural net: interpretability and robustness. Interpretability refers to the ability of humans to decipher why machines give a certain prediction. The ability to produce an answer even with mistakes in the data is called robustness. Usually, researchers focus on one or the other. Koo says:

"What my research is trying to do is bridge these two together because I don't think they're separate entities. I think that we get better interpretability if our models are more robust."

Koo hopes that if a machine can find robust and interpretable DNA patterns related to gene regulation, it will help geneticists understand how mutations affect cancer and other diseases.
-end-


Cold Spring Harbor Laboratory

Related Artificial Intelligence Articles from Brightsurf:

Physics can assist with key challenges in artificial intelligence
Two challenges in the field of artificial intelligence have been solved by adopting a physical concept introduced a century ago to describe the formation of a magnet during a process of iron bulk cooling.

A survey on artificial intelligence in chest imaging of COVID-19
Announcing a new article publication for BIO Integration journal. In this review article the authors consider the application of artificial intelligence imaging analysis methods for COVID-19 clinical diagnosis.

Using artificial intelligence can improve pregnant women's health
Disorders such as congenital heart birth defects or macrosomia, gestational diabetes and preterm birth can be detected earlier when artificial intelligence is used.

Artificial intelligence (AI)-aided disease prediction
Artificial Intelligence (AI)-aided Disease Prediction https://doi.org/10.15212/bioi-2020-0017 Announcing a new article publication for BIO Integration journal.

Artificial intelligence dives into thousands of WW2 photographs
In a new international cross disciplinary study, researchers from Aarhus University, Denmark and Tampere University, Finland have used artificial intelligence to analyse large amounts of historical photos from WW2.

Applying artificial intelligence to science education
A new review published in the Journal of Research in Science Teaching highlights the potential of machine learning--a subset of artificial intelligence--in science education.

New roles for clinicians in the age of artificial intelligence
New Roles for Clinicians in the Age of Artificial Intelligence https://doi.org/10.15212/bioi-2020-0014 Announcing a new article publication for BIO Integration journal.

Artificial intelligence aids gene activation discovery
Scientists have long known that human genes are activated through instructions delivered by the precise order of our DNA.

Artificial intelligence recognizes deteriorating photoreceptors
A software based on artificial intelligence (AI), which was developed by researchers at the Eye Clinic of the University Hospital Bonn, Stanford University and University of Utah, enables the precise assessment of the progression of geographic atrophy (GA), a disease of the light sensitive retina caused by age-related macular degeneration (AMD).

Classifying galaxies with artificial intelligence
Astronomers have applied artificial intelligence (AI) to ultra-wide field-of-view images of the distant Universe captured by the Subaru Telescope, and have achieved a very high accuracy for finding and classifying spiral galaxies in those images.

Read More: Artificial Intelligence News and Artificial Intelligence Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.