Within the past few years, models that can predict the structure or function of proteins have been widely used for a variety of biological applications, such as identifying drug targets and designing new therapeutic antibodies.

If you rotate an image of a molecular structure, a human can tell the rotated image is still the same molecule, but a machine-learning model might think it is a new data point. In computer science parlance, the molecule is “symmetric,” meaning the fundamental structure of that molecule remains the same if it undergoes certain transformations, like rotation.

In 1954, the world’s first successful organ transplant took place at Brigham and Women’s Hospital, in the form of a kidney donated from one twin to the other. At the time, a group of doctors and scientists had correctly theorized that the recipient’s antibodies were unlikely to reject an organ from an identical twin. One Nobel Prize and a few decades later, advancements in immune-suppressing drugs increased the viability of and demand for organ transplants. Today, over 1 million organ transplants have been performed in the United States, more than any other country in the world.

Understanding how molecules interact is central to biology: from decoding how living organisms function to uncovering disease mechanisms and developing life-saving drugs. In recent years, models like AlphaFold changed our ability to predict the 3D structure of proteins, offering crucial insights into molecular shape and interaction. But while AlphaFold could show how molecules fit together, it couldn’t measure how strongly they bind — a key factor in understanding all aforementioned. That missing piece is where MIT’s new AI model, Boltz-2, comes in. 

Given the recent explosion of large language models (LLMs) that can make convincingly human-like statements, it makes sense that there’s been a deepened focus on developing the models to be able to explain how they make decisions. But how can we be sure that what they’re saying is the truth?

Imagine a radiologist examining a chest X-ray from a new patient. She notices the patient has swelling in the tissue but does not have an enlarged heart. Looking to speed up diagnosis, she might use a vision-language machine-learning model to search for reports from similar patients.

The ambiguity in medical imaging can present major challenges for clinicians who are trying to identify disease. For instance, in a chest X-ray, pleural effusion, an abnormal buildup of fluid in the lungs, can look very much like pulmonary infiltrates, which are accumulations of pus or blood.