Thursday, September 17, 2026

 


Manuscripts-turned AI agents can now ‘talk’ to each other, make new discoveries



Papers, reimagined as AI collaborators


Stanford Medicine





Since 1665, scholarly journals have stood as written record of scientific advancement — static words on a page, a reference written by people for other people to read. That’s about to change.

A team of Stanford Medicine researchers led by postdoctoral scholar Jiacheng Miao, PhD, and associate professor of biomedical data science James Zou, PhD, designed an artificial intelligence program called Paper2Agent that turns any scientific manuscript — including the text, figures and data — into an interactive AI agent that can chat about the paper and interact with other paper agents.

“For essentially all of human history, the way that we represent knowledge is in the form of these very passive artifacts,” Zou said. “In old times people carved knowledge into stones, and now we type knowledge into words on pages — but in some sense pages aren’t that much better.”

Zou is programming a major update to the centuries-old practice of manuscript publishing. “This is an opportunity to fundamentally reimagine what knowledge looks like. Instead of having only passive artifacts, why don’t we convert each static record into an active embodiment of knowledge?” Zou said. Think of it, he said, like a virtual author who knows how that knowledge is generated — one that’s capable of explaining it and extending it by connecting with other papers and initiating new collaborations.

A paper describing the AI work will publish on Sept. 16 in Nature. Zou is the senior author, and Miao is the lead author.

Manuscripts manifested

The paper agents can answer questions about the work, apply methods from the paper to new data and even engage in conversations with other paper agents. The transformation from paper to AI agent starts with a team of bustling AI “worker agents” that pore over a single published paper and any associated code and data. But they’re not just reading the paper. What’s the best way to learn? Do it yourself.

The agents try to reproduce the original research from scratch. In a virtual environment, the agents simulate the research documented in the paper, and through that process, they capture the know-how a reader would otherwise have to dig out manually, from reagents needed to the experimental setup and execution.

The agents store that knowledge using something called an MCP, or model context protocol.

“An MCP lets AI essentially represent a paper PDF in a form that’s easy for agents to access, almost like a filing system,” Zou said. Each section of the paper is stored in a different folder, while the introduction, methods, results and conclusion are all organized into a separate file that lives in a parent file of a given paper.

AI does the heavy lifting, but Zou and the other human authors still have a role. The manuscript won’t capture things like failed experiments or judgment calls behind experimental setups. So humans have to supply that context to the paper agent in conversational exchanges in which the agent can question the authors about the paper and research.

AI-to-AI collaboration

A “live action” embodiment of knowledge can be a boon for readers of scientific manuscripts who seek to deeply understand the research, but these paper whisperers can do something even more impressive. They can talk to each other. That kind of agent-to-agent collaboration could become a vast research network — one with potential to make real discoveries.

Zou and his team demonstrated the power of agent-to-agent collaboration by converting two unrelated papers into agents. One described a tool for predicting how genetic mutations affect the genome; the other described a genome-wide association study of the risk of developing attention-deficit/hyperactivity disorder. With both papers spun up into agents, the two began to find common ground. The genome prediction agent applied its knowledge to the ADHD dataset and flagged a molecular variant near a gene called MPHOSPH9 that’s associated with increased ADHD risk — a connection that, according to Zou, had not been reported before.

“In the past, if there are two research groups that publish two different papers, those two research groups have to somehow find each other,” Zou said. With paper agents, that overlap can surface without human legwork. Zou’s team chose these two initial papers and paired them for this demonstration, but the eventual goal, he said, is something closer to manuscript speed dating at scale: Millions of paper agents surfacing common ground among themselves and working together to produce new insights.

Checking knowledge as it’s built

Zou is careful to note that attribution still matters. Agents that extend a paper’s reach are meant to help disseminate the original researchers’ work, not obscure whose work it is. “It’s still important to attribute the final discoveries and reference them back to original papers and original human authors,” he said.

Zou also noted that the parameters under which agents collaborate — and make new discoveries — should be closely guided and monitored to ensure the agents’ collaborations prioritize safety and ethical research.

The team is still expanding what a paper agent can do, including working out how, at scale, thousands or millions of these agents might productively find each other. Right now, the team has created more than 100 paper agents, but eventually, Zou hopes most manuscripts will have an associated paper agent. “Millions of papers are published every year,” he said. “There’s enormous potential here.”

This work was supported by funding from the Chan-Zuckerberg Biohub.

# # #

 

About Stanford Medicine

Stanford Medicine is an integrated academic health system comprising the Stanford School of Medicine and adult and pediatric health care delivery systems. Together, they harness the full potential of biomedicine through collaborative research, education and clinical care for patients. For more information, please visit med.stanford.edu.

 

Journal

DOI

Method of Research

Article Title

Article Publication Date

ChatGPT at university: What determines whether students will continue using it?

What really matters when it comes to using ChatGPT?

Beyond usefulness, trust is also key

DOI

Article Title

As AI enters health care, are we ready?


In new perspective piece, researchers call for health-literate AI




CUNY Graduate School of Public Health and Health Policy






New York, NY | September 16, 2026 – Artificial intelligence is rapidly becoming part of how people seek, interpret, and act on health information. Yet the technology is advancing faster than the evidence needed to determine whether these systems actually help people understand what matters, make informed health decisions, and know what to do next.

A new perspective led by University of Alabama Professor Rebecca K. Ivic, PhD, with CUNY SPH Distinguished Lecturer Scott C. Ratzan, MD and Emory University School of Medicine Professor Emerita Ruth M. Parker, MD, introduces the concept of health-literate artificial intelligence and proposes four principles for designing and governing AI-mediated health communication: comprehension, agency, accountability, and proportionality.

“We are deploying AI into health contexts faster than we are building the evidence needed to know whether it actually helps people understand, decide, and act,” says Dr. Ivic.

As AI systems are used to answer questions about symptoms, summarize health guidance, interpret risk and support decisions, a technically plausible response may be provided, while still failing to communicate how urgent a situation is, how certain the information is, what alternatives exist, when professional care is needed, and how to garner human judgment and dialogue for appropriate decision-making.

The authors define health-literate AI as AI designed to align information, guidance, and responsibility with users’ abilities, contexts, and needs. The framework shifts attention beyond whether AI produces information that is technically accurate or explainable to whether people can understand what that information means, make informed decisions, and determine what to do next.

The four components are:

  • Comprehension: Can people interpret AI output in relation to their language, prior knowledge, and circumstances?
  • Agency: Does the information support meaningful and informed action, including clear choices and next steps?
  • Accountability: Are evidence, uncertainty, limitations, and responsibility visible?
  • Proportionality: Does the amount and urgency of guidance match the stakes of the situation?

Together, these components provide a basis for considering whether AI-mediated communication is fit for purpose in health-relevant settings.

“Given all the discussion and warnings about the potential harms of AI, we need expert thinking, research, and analysis that protects people from potential harms while realizing the promise of this new technology for health,” says Dr. Ratzan, co-chair of the Nature Medicine Commission on Quality Health Information for All and editor-in-chief of the Journal of Health Communication.

“Is AI in healthcare the holy grail or the tower of Babel?” asks Dr. Parker. “In medicine, there are immediate questions: Can all people understand and safely use what these systems tell them in order to improve health outcomes? Is its use cost-effective and also aligned with our human values?”

The framework builds on decades of health literacy research that has increasingly examined not only individuals’ skills but also how governments, organizations, and systems make health information easier or harder to understand and use. For over 30 years, Drs. Parker and Ratzan have contributed substantially to this body of work, including research on health literacy as a systems and policy concern. Dr. Ivic proposes a novel model for today’s digital information environment, examining how platforms, institutions, and emerging technologies shape the production, interpretation, and use of health information.

Rather than placing the burden entirely on individuals to interpret increasingly complex automated information, health-literate AI asks how the design and governance of AI systems themselves can support understanding and informed action. The authors also challenge designers to envision how AI could help operationalize affordability of healthcare, a long-standing, well-acknowledged goal that we have not achieved.  

“This model gives researchers, developers, and regulators a shared way to address a more consequential question,” says Dr. Ivic, commissioner of the Nature Medicine Commission on Quality Health Information for All and executive editor of the Journal of Health Communication. “The question is not simply whether AI can generate an answer, but whether people can understand it, use it, and act on it appropriately. Health-literate AI should do more of the work of making quality health information understandable, actionable, and accountable, with design and governance working together to advance responsible AI in health.”

The authors argue that this is particularly important in high-stakes or ambiguous situations. AI systems should distinguish among informing, advising, and deciding and make those roles clear to users. When automated output is insufficient, systems should also identify when human judgment, clinical evaluation, or ethical deliberation is needed.

“The goal is not to make people better at navigating increasingly complex AI,” Ivic says. “It is to give the field a way to begin measuring whether that is actually happening.”

The perspective argues that health literacy should not simply require people to adapt to increasingly complex technologies. As AI becomes an increasingly important intermediary between people and health information, the systems themselves should be designed around the people who must understand and use them.

The authors call for adoption of the principles of health-literate AI to inform design, evaluation, research, and governance across health-relevant AI ecosystems. They also point to an important evidence gap: More research is needed to determine whether AI actually improves comprehension, informed decision-making, and health-related action.

“AI in healthcare no doubt offers opportunities for innovation, but more research, guardrails, and regulation are needed to ensure its benefits clearly outweigh its risks,” says Dr. Parker. “Its design and use needs to enhance users’ abilities to understand and make decisions that improve health, are affordable, and consistently aligned with our human values.”

Ivic, R.K., Ratzan, S.C. & Parker, R.M. Building health-literate artificial intelligence. Nat Hum Behav (2026).

Media contact:

Ariana Costakes

Communications Editorial Manager

ariana.costakes@sph.cuny.edu

About CUNY SPH

The CUNY Graduate School of Public Health and Health Policy (CUNY SPH) is committed to promoting and sustaining healthier populations in New York City and around the world through excellence in education, research, and service in public health and by advocating for sound policy and practice to advance social justice and improve health outcomes for all.

 

No comments: