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This Tool Turns Scientific Articles Into Agents That Answer Questions and Collaborate
The Paper2Agent system could make it easier to understand papers, reproduce results, and generate hypotheses.
For centuries, the humble scientific paper has been the way researchers share discoveries. These papers are highly formulaic. Each starts with an introduction laying out the problem, followed by hypotheses, results, and conclusions.
More recently, journals have asked authors to include code or datasets—like brain scans or gene activity—for others to inspect and reuse. Video and image summaries are now often welcome too.
But for the most part, papers haven’t changed much. They may tell an intriguing story—if you can get past all the jargon. And a PDF dozens of pages long makes it tough to reproduce results, often the first step in a new project. Human error can also leave out important pieces.
“For years, we have felt that static research papers are not the best way to represent scientific knowledge,” wrote James Zou at Stanford University. His team is about to shake things up. This month, they described Paper2Agent, a workflow that turns papers into interactive AI agents.
These aren’t your average chatbots. Each is trained on a paper’s text, figures, and data, and asked to reproduce its results, essentially running through the experiments in a virtual world. This gives them a deeper understanding of the work, turning them into virtual “authors” that can answer complex questions about it. They can also apply methods from one paper to a new dataset and even collaborate with other paper agents across disciplines.
There’s now “an opportunity to fundamentally reimagine what knowledge looks like,” Zou said in a press release. “Instead of having only passive artifacts, why don’t we convert each static record into an active embodiment of knowledge?”
Embarrassment of RichesThe volume of scientific publishing has skyrocketed in recent decades. Global scientific output topped three million papers in 2023, and the numbers are still climbing.
That much literature would overwhelm anyone. Yet reading papers to build up foundational knowledge is the first step in any scientific project. The challenge is even thornier when research crosses disciplines—say AI and protein science, or machine consciousness and neuroscience. In these cases, scientists must master multiple fields, but the connections they form often spark breakthroughs.
The sheer volume creates another headache: reproducibility. Scientists are a critical bunch. Before building on a previous paper’s conclusions, they often try to recreate the experiment to see if they get the same results.
It doesn’t always work. In the landmark 2015 Reproducibility Project, only 39 percent of psychology studies produced results consistent with their original findings. A 2026 analysis didn’t fare much better. And large language models may add a wrinkle in machine learning research, where the pipeline, from data collection to model selection and training, isn’t always well documented.
For Zou and team, turning papers into AI agents could help us tackle these problems.
‘Living’ KnowledgeTo develop Paper2Agent, the team first ask it to scan all sections of a paper and then try to recreate its results. Along the way, it captures details that a reader might otherwise have to dig out, such as experimental setups and chemicals, and saves them in a digital vault called an MCP server.
Anthropic developed MCP to give AI systems access to tools, data, and workflows through a common interface. Scientists can then link a large language model of their choice to the server, query the agent in everyday language, or run new experiments using their own data while borrowing the paper’s methods.
In other words, Paper2Agent is like a translator between a human-written paper and a chatbot.
That might sound redundant. After all, it’s already possible to upload a paper to ChatGPT, Claude, or another chatbot and ask questions. The difference is in the training: A chatbot can summarize a paper’s results, but it doesn’t have a deeper understanding of how those results came to be or whether the underlying analysis holds up.
By trying to replicate results based on the paper, Paper2Agent’s AI gets a sort of hands-on experience, potentially making it less prone to hallucination. The agents can “provide much more in-depth insights to the readers,” Zou told Nature.
In one experiment, Paper2Agent created an agent based on a recent paper describing AlphaGenome, an AI model that predicts how changes in DNA letters affect their function. It took under an hour without human supervision.
When asked genetics questions requiring AlphaGenome analysis, the agent answered with near-perfect accuracy. It was also two to four times faster than Biomi and other “AI scientists” given access to the same paper, likely because it had a better grasp of AlphaGenome’s tools and capabilities.
The tool didn’t always work. When the team applied it to 110 papers spanning computational biology, machine learning, astrophysics, and other fields, it successfully converted 76 percent into working agents. But that failure is arguably a feature, not a bug. Papers that couldn’t be agentified often lacked sufficient code, data, or model files, or relied on broken scripts and unavailable datasets.
“Agentification can therefore serve as a practical diagnostic of computational reproducibility,” wrote Zou and study author Jiacheng Miao.
Digital CollaborationLeft alone, the agents began “talking” to each other.
In one test, Paper2Agent converted two studies on psoriasis into agents. Working with the AlphaGenome agent, the trio found a previously unknown genetic variant as a potential cause for the condition. An agent based on a paper about ADHD genetics similarly flagged a new mutation associated with increased risk. Another pair of agents identified a DNA letter variant linked to “bad” cholesterol, one that AlphaGenome had not pinpointed on its own.
These results showcase the power of collaboration in a world where papers aren’t isolated documents. “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. Paper agents could make that matchmaking automatic, allowing findings from different studies to mesh—and produce new ideas—with far less human effort.
Paper2Agent is free to use, although installing and running it still needs some computer savvy scientists may not have. For trainees, it could become a shortcut that stunts their ability to critically evaluate a paper and spot flaws in the authors’ logic, instead taking an agent’s reply at face value.
Other questions remain. If agents become a new way of sharing scientific knowledge, who should be responsible for creating them? And can papers based primarily on wet-lab experiments, rather than code, also benefit?
Magdalena Skipper, editor-in-chief of Nature, which published the work, doesn’t expect conventional papers to disappear anytime soon. But she is optimistic that agentifying papers could alter the future of sharing scientific knowledge.
“There is a prospect that…there will be something genuinely influential that will change the way knowledge is disseminated, but importantly, the way that knowledge is interacted with,” she said.
The post This Tool Turns Scientific Articles Into Agents That Answer Questions and Collaborate appeared first on SingularityHub.
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Microsoft will let Copilot act on local files on Windows PCs
Microsoft is giving Copilot greater control over Windows PCs, allowing the AI assistant to organize and make changes to local files, and run certain tasks using on-device AI models.
The changes were announced at Microsoft’s Hybrid Intelligence event, where it outlined plans to combine local and cloud AI processing to help customers reduce AI costs and retain more control over data.
Three new Copilot capabilities will be available to Copilot+ PC users “in the coming months,” Microsoft said.
One is the ability for Copilot to access local files and recent user activity, providing additional context for the AI assistant’s outputs.
Copilot will also be able to perform actions on a device, such as moving files and changing settings.
“It has the same level of the ability to control and change things that I do as a user, but always with permission,” said Jacob Andreou, Microsoft EVP, Copilot, during the event.
The capability sounds similar to Copilot Actions, an “experimental” feature that Microsoft announced last year in preview for Windows Insiders at the time.
Finally, there will be an option to run Copilot on local AI models for certain tasks, only accessing cloud servers “when needed,” Microsoft said.
“Copilot will still use the cloud for the hardest tasks,” said Andreou, “but for times when cost or privacy matter more, it can delegate down to local models that run directly on your computer.”
Microsoft’s hybrid model reflects market demand, noted Biswajeet Mahapatra, principal analyst at Forrester. “The demand we see is not for AI that runs exclusively on-device, but for AI that can intelligently decide which workloads should run locally and which belong in the cloud,” Mahapatra said. “Enterprises increasingly want both options available.”
In a demo, Andreou also showed how the ability to access and interact with local files will increase the usefulness of Autopilot (formerly called Scout), the long-running Copilot agent that can be set to work continuously in the background. (Autopilot is currently in private preview.) Autopilot can also run on locally hosted models, he added, helping reduce costs and avoid sending private data to the cloud.
Microsoft also announced more powerful hardware — including the Surface Laptop Ultra and Surface RTX Spark Dev Box — and more efficient AI models designed to run on devices.
“Most companies are still getting their heads around AI, token usage, which models to use, and where to run them,” said Tom Mainelli, group vice president, Device & Consumer Research, at IDC. “As these companies get more savvy and look to scale AI to more employees, the need to run AI locally — including Microsoft Copilot — will increase.”
Current business laptops have some local AI capabilities and features, said Mainelli, but still largely rely on Copilot running in the cloud. This could change once more advanced hardware is broadly available, he said.
“As more systems ship with the right combination of CPU, GPU, NPU, and memory, and as local models continue to improve, I expect more AI jobs to run on the device,” said Mainelli.
For now, the installed base of enterprise PCs “remains highly mixed,” said Mahapatra.
“While Microsoft highlighted new AI-capable hardware, and noted that a growing share of business laptops are Copilot+ PCs, most enterprise fleets will take several years to refresh,” he said.
“The immediate opportunity is therefore concentrated among organizations already investing in AI PCs and high-performance devices. Many enterprises will continue to rely primarily on cloud-hosted AI while selectively adopting local AI capabilities as refresh cycles progress.”
Microsoft is also attempting to address security when running agents on-device. This includes the general availability launch of Microsoft Execution Containers (MXC) on Windows 11, which allows organizations to set up policies that define which files and networks agents can access. MXC is supported by a range of agent tools, including OpenAI’s Codex and OpenClaw, with Anthropic Claude Code, Box, Manus, and others to follow.
Added security measures should give business customers more confidence when enabling Copilot to access local files, said Mainelli. “That’s what Microsoft is bringing to the table: a level of security and traceability in these processes that should give companies confidence in using them,” he said. “Microsoft took major steps in telling that story today, and we’ll see how companies respond.”
Enterprises should manage agents on Windows devices “in the same way they approach any automation platform: trust should be based on controls, not on the AI itself,” said Mahapatra.
“Microsoft’s announcement is significant because it acknowledges that agents require a different security model than traditional applications,” he said. “Technologies such as Microsoft Execution Containers are designed to limit what agents can access, identify which agent took an action, and enforce policy-based controls.”
At the same, he warned against granting broad autonomous access to local files without appropriate governance. “Role-based access, read-only assistance, document summarization, search, and workflow support are likely to be adopted more quickly than autonomous file modification or business process execution,” Mahapatra said.
“As agents move from providing recommendations to taking actions, organizations will need stronger approval controls, monitoring, auditing, and human oversight. This is especially important for agents interacting with sensitive data, regulated processes, or systems of record.”
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Fast AI, slow rollback: the risk facing Apple IT teams
There’s a big disconnect between the rate at which IT is deploying various kinds of AI-generated output and the speed with which it can roll those changes back when things go wrong, warns a new report from Fleet Device Management. It’s almost as if the rush to embrace AI has eclipsed the need to manage its deployment effectively.
The research, based on a survey of more than 250 enterprise IT practitioners managing Apple devices, is available in full via the company’s website and echoes similar concerns I’ve heard from others in the space. I spoke with Fleet founder and CEO Mike McNeil to get his take on the disconnect.
What’s happening in the enterpriseFirst, some of the stats gathered in the survey:
- 86% of respondents allow AI-written output to reach production devices following some review.
- 61% used AI to author an MDM profile/configuration in the past month.
- 62% used it to write scripts/code.
- 69% can’t roll back a bad configuration within an hour; 43% need more than a day.
- About a quarter (26%) can recover the same day but only with manual intervention.
McNeil stressed the challenge exposed by this data. “When one of those changes is wrong, 69% can’t undo it within an hour, and 43% need more than 24 hours,” he said. “So the exposure is real even without a count of incidents. The AI tool isn’t what gets pulled back. The configuration it produced is, and most teams do that by hand.”
The risk of moving too fastHe told me that just 7.6% of Fleet’s customers are exclusively Mac shops, confirming that most Fleet clients manage multiple platforms. It’s not a platform-specific challenge; McNeil sees this as a problem for all of them.
“I’d frame risk by two things: how much privilege the code runs with and how hard recovery is,” he explained, noting the risk of scripts running at root, which can take full control of the machine to the extent that reversion can’t undo what’s done.
“Windows and Linux have the most scripting-heavy management, so they have the most room for script-level mistakes,” he said — but even iOS is at risk from a bad restriction or network profile, particularly when attempting to recover remotely.
He pointed out: “36% of respondents manage Apple devices through Intune, a Windows-first platform. Tooling built around one platform’s assumptions tends to be weakest at the edges of another’s.”
Why MDM is a high-risk toolFor Apple in the enterprise, the risk is inherent to device management and IT’s power to use MDM to deploy a potentially poorly crafted AI tool at scale.
“MDM is one of the few trusted paths that can bypass the [macOS platform security] prompts, which is exactly why a bad or malicious MDM-delivered change is so consequential,” he warned.
He continued: “Windows has a larger and older attack ecosystem, with more legacy surface area. Linux gives administrators the most freedom and the fewest guardrails. On every platform, the management channel is the high-value target, so the same controls apply — review, least privilege, a change record, and a fast revert.”
The risk is that poorly crafted AI-generated MDM profiles can set off a chain of problems that can take days to resolve, particularly in large-scale device deployments. The problem is that unless there’s a clear audit record, it’s harder to remediate errors.
“AI speeds up authoring, but review capacity stays the same,” McNeil said. “Without a gate, errors and anything malicious in a script reach production faster.”
Speed needs to be managedUltimately, while AI can accelerate a multitude of IT tasks, the speed of deployment must also be matched by robust review and strong rollback tools. “Speed is only an advantage if recovery keeps pace,” he said.
Fleet’s core argument is that IT needs to change how it approaches what it does. “Mac administration is an engineering discipline now, and these admins are further along than the industry thinks,” he said. “The infrastructure around them hasn’t caught up.”
How should IT approach this? McNeil suggests a succession of protections his own MDM system already supports through GitOps with YAML files, adding, “the pattern works with any tool that has an API.”
- Treat device configuration like application code.
- Profiles, scripts, and policies should live as files in a Git repository.
- A change arrives as a pull request, a second person reviews it, and automation applies it to devices.
- To undo it, you revert the commit.
“One caveat: a revert fixes what the configuration says. It doesn’t undo a script that has already run. That’s an argument for preferring declarative configuration over imperative scripts where you can,” he advised.
Less clicking, more engineeringNone of these cautions are arguments against use of AI in enterprise IT, of course. They are arguments to promote a more conscious management system around the use of it. All the same, as AI proliferates, the Fleet CEO does think IT pros must anticipate a change in their roles. “Less clicking, more engineering,” he said.
“As AI takes on more of the mechanics like creating configuration profiles, drafting scripts, and troubleshooting routine issues, admins can spend less time figuring out how to make a change and more time deciding what should change, how it affects the business and where human judgment is required,” he said.
Finally, I pointed to the ongoing dilemma between Apple and IT. Some people complain Apple doesn’t innovate in the enterprise fast enough, others say it innovates too fast. What does Fleet think?
“Keeping up with Apple’s release pace was the single most cited hardest part of the job, at 31%,” he told me. “Budget and headcount came last, at 5%. Admins aren’t complaining that Apple ships too little. They’re stretched by the yearly OS cycle, new frameworks, and deprecations.”
“My own view is that the direction is right,” he said. “Declarative Device Management and tighter platform security are good for enterprises. The pace is the issue, and it’s the main reason admins need automation and a safety net.”
Now please subscribe to my daily, human-curated Apple-related news headline feed at The Core, or follow me on BlueSky, LinkedIn, or Mastodon.
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