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How scientists are using arti cial intelligence

It is already making research faster, better, and more productive

image: shira inbar

Sep 13th 2023

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I n 2019, scientists at the Massachusetts Institute of Technology (mit) did

something unusual in modern medicine—they found a new antibiotic,
halicin. In May this year another team found a second antibiotic, abaucin. What
marked these two compounds out was not only their potential for use against
two of the most dangerous known antibiotic-resistant bacteria, but also how
they were identi ed.

In both cases, the researchers had used an arti cial-intelligence (ai) model to
search through millions of candidate compounds to identify those that would
work best against each “superbug”. The model had been trained on the chemical
structures of a few thousand known antibiotics and how well (or not) they had
worked against the bugs in the lab. During this training the model had worked
out links between chemical structures and success at damaging bacteria. Once
the ai spat out its shortlist, the scientists tested them in the lab and identi ed
their antibiotics. If discovering new drugs is like searching for a needle in a
haystack, says Regina Barzilay, a computer scientist at mit who helped to nd
abaucin and halicin, ai acts like a metal detector. To get the candidate drugs
from lab to clinic will take many years of medical trials. But there is no doubt
that ai accelerated the initial trial-and-error part of the process. It changes what
is possible, says Dr Barzilay. With ai, “the type of questions that we will be
asking will be very di erent from what we’re asking today.”

Drug discovery is not alone in being jolted by the potential of ai. Researchers
tackling many of the world’s most complicated and important problems—from
forecasting weather to searching for new materials for batteries and solar panels
and controlling nuclear-fusion reactions—are all turning to ai in order to
augment or accelerate their progress.

The potential is enormous. “ai could usher in a new renaissance of discovery,”

argues Demis Hassabis, co-founder of Google DeepMind, an ai lab based in
London, “acting as a multiplier for human ingenuity.” He has compared ai to the
telescope, an essential technology that will let scientists see farther and
understand more than with the naked eye alone.

Where have you been?

image: the economist

Though it has been part of the scienti c toolkit since the 1960s, for most of its
life ai has been stuck within disciplines where scientists were already well-
versed in computer code—particle physics, for example, or mathematics. By
2023, however, with the rise of deep learning, more than 99% of research elds
were producing ai-related results, according to csiro, Australia’s science agency
(see chart). “Democratisation is the thing that is causing this explosion,” says
Mark Girolami, chief scientist at the Alan Turing Institute in London. What used
to require a computer-science degree and lines of arcane programming
languages can now be done with user-friendly ai tools, often made to work after
a query to Chatgpt, Openai’s chatbot. Thus scientists have easy access to what is
essentially a dogged, superhuman research assistant that will solve equations
and tirelessly sift through enormous piles of data to look for any patterns or
correlations within.

In materials science, for example, the problem is similar to that in drug

discovery—there are an unfathomable number of possible compounds. When
researchers at the University of Liverpool were looking for materials that would
have the very speci c properties required to build better batteries, they used an
ai model known as an “autoencoder” to search through all 200,000 of the
known, stable crystalline compounds in the Inorganic Crystal Structure
Database, the world’s largest such repository. The ai had previously learned the
most important physical and chemical properties required for the new battery
material to achieve its goals and applied those conditions to the search. It
successfully reduced the pool of candidates for scientists to test in the lab from
thousands to just ve, saving time and money.

The nal candidate—a material combining lithium, tin, sulphur and chlorine—
was novel, though it is too soon to tell whether or not it will work commercially.
The ai method, however, is being used by researchers to discover other sorts of
new materials.

What did you dream?

ai can also be used to predict. The shapes into which proteins twist themselves
after they are made in a cell are vital to making them work. Scientists do not yet
know how proteins fold. But in 2021, Google DeepMind developed AlphaFold, a
model that had taught itself to predict the structure of a protein from its amino-
acid sequence alone. Since it was released, AlphaFold has produced a database of
more than 200m predicted protein structures, which has already been used by
over 1.2m researchers. For example, Matthew Higgins, a biochemist at the
University of Oxford, used AlphaFold to gure out the shape of a protein in
mosquitoes that is important for the malaria parasite that the insects often carry.
He was then able to combine the predictions from AlphaFold to work out which
parts of the protein would be the easiest to target with a drug. Another team used
AlphaFold to nd—in just 30 days—the structure of a protein that in uences
how a type of liver cancer proliferates, thereby opening the door to designing a
new targeted treatment.

AlphaFold has also contributed to the understanding of other bits of biology. The
nucleus of a cell, for example, has gates to bring in material to produce proteins.
A few years ago, scientists knew the gates existed, but knew little about their
structure. Using AlphaFold, scientists predicted the structure and contributed to
understanding about the internal mechanisms of the cell. “We don’t really
completely understand how [the ai] came up with that structure,” says Pushmeet
Kohli, one of AlphaFold’s inventors who now heads Google DeepMind’s “ai for
Science” team “But once it has made the structure it is actually a foundation
Science team. But once it has made the structure, it is actually a foundation
that now, the whole scienti c community can build on top of.”

ai is also proving useful in speeding up complex computer simulations. Weather

models, for example, are based on mathematical equations that describe the
state of Earth’s atmosphere at any given time. The supercomputers that forecast
weather, however, are expensive, consume a lot of power and take a lot of time to
carry out their calculations. And models must be run again and again to keep up
with the constant in ow of data from weather stations around the world.

Climate scientists, and private companies, are therefore beginning to deploy

machine learning to speed things up. Pangu-Weather, an ai built by Huawei, a
Chinese company, can make predictions about weather a week in advance
thousands of times faster and cheaper than the current standard, without any
meaningful dip in accuracy. FourCastNet, a model built by Nvidia, an American
chipmaker, can generate such forecasts in less than two seconds, and is the rst
ai model to accurately predict rain at a high spatial resolution, which is
important information for predicting natural disasters such as ash oods. Both
these ai models are trained to predict the weather by learning from
observational data, or the outputs of supercomputer simulations. And they are
just the start—Nvidia has already announced plans to build a digital twin of
Earth, called “Earth-2”, a computer model that the company hopes will be able to
predict climate change at a more regional level, several decades in advance.

Physicists trying to harness the power of nuclear fusion, meanwhile, have been
using ai to control complex bits of kit. One approach to fusion research involves
creating a plasma (a superheated, electrically charged gas) of hydrogen inside a
doughnut-shaped vessel called a tokamak. When hot enough, around 100m°C,
particles in the plasma start to fuse and release energy. But if the plasma touches
the walls of the tokamak, it will cool down and stop working, so physicists
contain the gas within a magnetic cage. Finding the right con guration of
magnetic elds is endishly di cult (“a bit like trying to hold a lump of jelly
with knitting wool”, according to one physicist) and controlling it manually
requires devising mathematical equations to predict what the plasma will do
and then making thousands of small adjustments every second to around ten
di erent magnetic coils. By contrast, an ai control system built by scientists at
Google DeepMind and epfl in Lausanne, Switzerland, allowed scientists to try
out di erent shapes for the plasma in a computer simulation—and the ai then
worked out how best to get there
worked out how best to get there.

Automating and speeding up physical experiments and laboratory work is

another area of interest. “Self-driving laboratories” can plan an experiment,
execute it using a robotic arm, and then analyse the results. Automation can
make discovering new compounds, or nding better ways of making old
compounds, up to a thousand times faster.

You’ve been in the pipeline

Generative ai, which exploded into public consciousness with the arrival of
Chatgpt in 2022 but which scientists have been playing with for much longer,
has two main scienti c uses. First, it can be used to generate data. “Super-
resolution” ai models can enhance cheap, low-resolution electron-microscope
images into high-resolution ones that would otherwise have been too expensive
to record. The ai compares a small area of a material or a biological sample in
high resolution with the same thing recorded at a lower resolution. The model
learns the di erence between the two resolutions and can then translate
between them.
And just as a large language model (llm) can generate uent sentences by
predicting the next best word in a sequence, generative molecular models are
able to build molecules, atom by atom, bond by bond. llms use a mix of self-
taught statistics and trillions of words of training text culled from the internet to
write in ways that plausibly mimic a human. Trained on vast databases of known
drugs and their properties, models for “de novo molecular design” can gure out
which molecular structures are most likely to do which things, and they build
accordingly. Verseon, a pharmaceutical company based in California, has
created drug candidates in this way, several of which are now being tested on
animals, and one—a precision anticoagulant—that is in the rst phase of
clinical trials. Like the new antibiotics and battery materials identi ed by ai,
chemicals designed by algorithms will also need to undergo the usual trials in
the real world before their e ectiveness can be assessed.

A more futuristic use for llms comes from Igor Grossmann, a psychologist at the
University of Waterloo. If an llm could be prompted with real (or fabricated)
back stories so as to mirror accurately what human participants might say, they
could theoretically replace focus groups, or be used as agents in economics
research. llms could be trained with various di erent personas, and their
behaviour could then be used to simulate experiments, whose results, if
interesting, could later be con rmed with human subjects.

llms are already making scientists themselves more e cient. According to

GitHub, using tools like its “Copilot” can help coders write software 55% faster.
For all scientists, reading the background research in a eld before embarking
on a project can be a daunting task—the sheer scale of the modern scienti c
literature is too vast for a person to manage. Elicit, a free online ai tool created
by Ought, an American non-pro t research lab, can help by using an llm to
comb through the mountains of research literature and summarise the
important ones much faster than any human could. It is already used by
students and younger scientists, many of whom nd it useful to nd papers to
cite or to de ne a research direction in the face of a mountain of text. llms can
even help to extract structured information—such as every experiment done
using a speci c drug—from millions of documents.

Widening access to knowledge within disciplines could also be achieved with ai.
Each detector at the Large Hadron Collider at cern in Geneva requires its own
specialised teams of operators and analysts. Combining and comparing data
from them is impossible without physicists from each detector coming together
to share their expertise. This is not always feasible for theoretical physicists who
want to quickly test new ideas. Miguel Arratia, a physicist at the University of
California, Riverside, has therefore proposed using ai to integrate
measurements from multiple fundamental physics experiments (and even
cosmological observations) so that theoretical physicists can quickly explore,
combine and re-use the data in their own work.

ai models have demonstrated that they can process data, and automate
calculations and some lab work (see table). But Dr Girolami warns that whereas
ai might be useful to help scientists ll in gaps in knowledge, the models still
struggle to push beyond the edges of what is already known. These systems are
good at interpolation—connecting the dots—but less so at extrapolation,
imagining where the next dot might go.

And there are some hard problems that even the most successful of today’s ai
systems cannot yet handle AlphaFold for example does not get all proteins
systems cannot yet handle. AlphaFold, for example, does not get all proteins
right all the time. Jane Dyson, a structural biologist at the Scripps Research
Institute in La Jolla, California, says that for “disordered” proteins, which are
particularly relevant to her research, the ai’s predictions are mostly garbage. “It’s
not a revolution that puts all of our scientists out of business.” And AlphaFold
does not yet explain why proteins fold in the ways they do. Though perhaps the
ai “has a theory we just have not been able to grasp yet,” says Dr Kohli.

image: shira inbar

Despite those limitations, structural biologists still reckon that AlphaFold has
made their work more e cient. The database lled with AlphaFold’s protein
predictions allows scientists to work out the likely structure of a protein in a few
seconds, as opposed to the years and tens of thousands of dollars it might have
taken otherwise.

And speeding up the pace of scienti c research and discovery, making

e ciencies wherever possible, holds plenty of promise. In a recent report on ai
in science the oecd, a club of rich countries, said that “while ai is penetrating all
domains and stages of science, its full potential is far from realised.” The prize, it
concluded, could be enormous: “Accelerating the productivity of research could
be the most economically and socially valuable of all the uses of arti cial
intelligence.”
Welcome to the machine
If ai tools manage to boost the productivity of research, the world would no
doubt get the “multiplier for human ingenuity” predicted by Dr Hassabis. But ai
holds more potential still: just like telescopes and microscopes let scientists see
more of the world, the probabilistic, data-driven models used in ai will
increasingly allow scientists to better model and understand complex systems.
Fields like climate science and structural biology are already at the point where
scientists know that complicated processes are happening, but researchers so far
have mainly tried to understand those subjects using top-down rules, equations
and simulations. ai can help scientists approach problems from the bottom up
instead—measure lots of data rst, and use algorithms to come up with the
rules, patterns, equations and scienti c understanding later.

If the past few years have seen scientists dip their toes into the shallow waters of
ai, the next decade and beyond will be when they have to dive into its depths
and swim towards the horizon. 7

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This article appeared in the Science & technology section of the print edition under the headline "Faster, better,
more productive"

Science & technology

September 16th 2023

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