COLD
SPRING HARBOR, N.Y., June 21,
2024 /PRNewswire/ -- Artificial intelligence
continues to squirm its way into many aspects of our lives. But
what about biology, the study of life itself? AI can sift through
hundreds of thousands of genome data points to identify potential
new therapeutic targets. While these genomic insights may appear
helpful, scientists aren't sure how today's AI models come to their
conclusions in the first place. Now, a new system named SQUID
arrives on the scene armed to pry open AI's black box of murky
internal logic.
SQUID, short for Surrogate Quantitative Interpretability for
Deepnets, is a computational tool created by Cold Spring Harbor
Laboratory (CSHL) scientists. It's designed to help interpret how
AI models analyze the genome. Compared with other analysis tools,
SQUID is more consistent, reduces background noise, and can lead to
more accurate predictions about the effects of genetic
mutations.
How does it work so much better? The key, CSHL Assistant
Professor Peter Koo says, lies
in SQUID's specialized training. Koo explains:
"The tools that people use to try to understand these models
have been largely coming from other fields like computer vision or
natural language processing. While they can be useful, they're not
optimal for genomics. What we did with SQUID was leverage decades
of quantitative genetics knowledge to help us understand what these
deep neural networks are learning."
SQUID works by first generating a library of over 100,000
variant DNA sequences. It then analyzes the library of mutations
and their effects using a program called MAVE-NN (Multiplex Assays
of Variant Effects Neural Network). This tool allows scientists to
perform thousands of virtual experiments simultaneously. In effect,
they can "fish out" the algorithms behind a given AI's most
accurate predictions. Their computational "catch" could set the
stage for experiments that are more grounded in reality. CSHL
Associate Professor Justin Kinney, a
co-author of the study, explains:
"In silico [virtual] experiments are no replacement for actual
laboratory experiments. Nevertheless, they can be very informative.
They can help scientists form hypotheses for how a particular
region of the genome works or how a mutation might have a
clinically relevant effect."
There are tons of AI models in the sea. More enter the waters
each day. Koo, Kinney, and colleagues hope that SQUID will help
scientists grab hold of those that best meet their specialized
needs.
Though mapped, the human genome remains an incredibly
challenging terrain. SQUID could help biologists navigate the field
more effectively, bringing them closer to their findings' true
medical implications.
About Cold Spring Harbor Laboratory
Founded in 1890,
Cold Spring Harbor Laboratory has shaped contemporary biomedical
research and education with programs in cancer, neuroscience, plant
biology and quantitative biology. Home to eight Nobel Prize
winners, the private, not-for-profit Laboratory employs 1,000
people including 600 scientists, students and technicians. For more
information, visit www.cshl.edu
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SOURCE Cold Spring Harbor Laboratory