Artificial Intelligence continues to weave its way into various facets of our everyday life, including the field of biology where it has shown immense potential. AI applications provide the ability to sift through humongous genomic data to identify new therapeutic targets. Although this potential is promising, the process by which current AI models reach their conclusions remains unclear. To make this process transparent, a new tool known as SQUID has seen the light of day and is ready to decode the mysterious inner workings of this AI black box.
SQUID, which stands for 'Surrogate Quantitative Interpretability for Deepnets', is a computational tool designed by the scientists of Cold Spring Harbor Laboratory (CSHL). This tool aims to unveil how AI models analyze genomic data. On comparison with other such analytical tools, SQUID stands out with its consistency, ability to reduce noise, and improved accuracy in predicting the effects of genetic mutations.
SQUID's unique training methodology plays the primary role in enhancing its effectiveness. As explained by CSHL Assistant Professor Peter Koo, existing tools used to interpret AI models are derived from different fields like computer vision or natural language processing, which might not be applicable for genetic analysis. Rather than working with a "one size fits all" solution, SQUID uses a plethora of knowledge from quantitative genetics to help understand what these deep learning models have learned.
Operating on a unique mechanism, SQUID generates a library of over 100,000 variant DNA sequences. These variant sequences are then analyzed by a program called MAVE-NN (Multiplex Assays of Variant Effects Neural Network). MAVE-NN is a powerful tool that enables scientists to perform thousands of simultaneous virtual experiments. As a result, researchers are able to identify the algorithms behind an AI's most accurate predictions, setting the stage for experiments grounded in reality.
Echoing this sentiment, CSHL Associate Professor Justin Kinney, co-author of the study, emphasized that these in silico (virtual) experiments can't replace actual laboratory experiments but can offer significant insights. Such virtual studies provide scientists with fundamental hypotheses regarding how certain regions of the genome function, or how a particular mutation might impact clinical relevance.
The influx of new AI models into the field adds new fish to the computational sea every day. The creators of SQUID hope that this tool will help scientists reel in the models that are most suited to their specific requirements.
While the terrain of the human genome is thoroughly mapped, navigating it remains a daunting challenge. SQUID is poised to become invaluable for biologists, helping them traverse this complex terrain with increased effectiveness and precision, leading them closer to deciphering the true medical implication of their research findings.
Disclaimer: The above article was written with assistance from an AI tool. The original sources can be found on ScienceDaily.
