Creating a virtual brain may sound like a science-fiction nightmare, but for neuroscientists in Japan and at Seattle’s Allen Institute, it’s a big step toward a long-held dream.

They say their mouse-cortex simulation, run on one of the world’s fastest supercomputers, could eventually open the way to understanding the mechanisms behind maladies such as Alzheimer’s disease and epilepsy — and perhaps unraveling the mysteries of consciousness.

“This shows the door is open,” Allen Institute investigator Anton Arkhipov said today in a news release. “It’s a technical milestone giving us confidence that much larger models are not only possible, but achievable with precision and scale.”

Arkhipov and his colleagues describe the project in a research paper being presented this week in St. Louis during the SC25 conference on high-performance computing. The simulation models the activity of a whole mouse cortex, encompassing nearly 10 million neurons connected by 26 billion synapses.

To create the simulation, researchers fed data from the Allen Cell Types Database and the Allen Connectivity Atlas into Supercomputer Fugaku, a computing cluster developed by Fujitsu and Japan’s RIKEN Center for Computational Science. Fugaku is capable of executing more than 400 quadrillion operations per second, or 400 petaflops.

The massive data set was translated into a 3-D model using the Allen Institute’s Brain Modeling ToolKit. A simulation program called Neulite brought the data to life as virtual neurons that interact with each other like living brain cells.

Scientists ran the program in different scenarios, including an experiment that used the full-scale Fugaku configuration to model the entire mouse cortex.

“In our simulation, each neuron is modeled as a large tree of interacting compartments — hundreds of compartments per neuron,” Arkhipov said in comments emailed to GeekWire. “That is, we are capturing some sub-cellular structures and dynamics within each neuron.”

During the full-scale simulation, it took no more than 32 seconds to simulate one second of real-time activity in a living mouse brain. “This level of performance — 32 times slower than real time — is quite impressive for a system of this size and complexity,” Arkhipov said. “It is not uncommon to see a factor of thousands of times slower for such very detailed simulations (even much smaller than ours).”

The researchers acknowledge that much more work is needed to turn their simulation into a model capable of tracing the progress of a neurological disease. For example, the model doesn’t reflect brain plasticity — that is, the brain’s ability to rewire its own connections.

“If we want to mention something specific besides plasticity, then one aspect that is missing is the effects of neuromodulators, and the other is that we currently do not have a very detailed representation of sensory inputs in our whole-cortex simulations,” Arkhipov said. “For all of these, we need much more data than currently available to make much better models, although some approximations or hypotheses could be implemented and tested now that we have a working whole-cortex simulation.”

Arkhipov said the project’s long-term goal is to simulate an entire brain, not just the cortex. “There’s a distinction between whole-cortex and whole-brain,” he pointed out. “The mouse cortex (and our model of it) contains about 10 million neurons, whereas the whole mouse brain contains about 70 million neurons.”

A human-brain simulation would require an even greater leap. The human cortex alone contains not just 10 million neurons, but 21 billion.

The good news is that a sufficiently powerful supercomputer might be up to the task. “Our work shows that very detailed microscopic-level simulations of larger brains may be possible sooner than previously expected,” Arkhipov said. “The results suggest that a simulation of the whole monkey brain (such as that of a macaque monkey with 6 billion neurons) can fit on the full-scale Fugaku system.”

Arkhipov said it was important to point out that creating a brain model on a supercomputer “does not mean that such a model is complete or accurate.”

“Here we are talking about technical feasibility of simulations, and it looks like such simulations even at the scale of the monkey brain are now within reach,” he said. “But to make such simulations biologically realistic, much more experimental data production and model building work would need to happen.”

Rin Kuriyama and Kaaya Akira of the University of Electro-Communications in Tokyo are the principal authors of the paper presented at SC25, titled “Microscopic-Level Mouse Whole Cortex Simulation Composed of 9 Million Biophysical Neurons and 26 Billion Synapses on the Supercomputer Fugaku.” In addition to Arkhipov, authors from the Allen Institute include Laura Green, Beatriz Herrera and Kael Dai. The study’s other authors are Tadashi Yamazaki and Mari Iura of the University of Electro-Communications; Gilles Gouaillardet and Asako Terasawa of the Research Organization for Information Science and Technology in Hyogo, Japan; Taira Kobayashi of Yamaguchi University; and Jun Igarashi of the RIKEN Center for Computational Science.

The Allen Institute in Seattle has released the Brain Knowledge Platform, a research aid described as the most comprehensive artificial intelligence tool available for neuroscience.

The project aims to unify brain information from dozens of collaborators, species (such as humans, other primates and mice), and samples that span early development to old age, encompassing diverse data including cell types and disease indicators.

Using AI, this data has been translated into a shared scientific language or format, allowing for “apples-to-apples” comparisons across institutions and organisms to create a much larger dataset for new insights.

“Understanding the brain is not a single institute’s effort,” said Shoaib Mufti, the Allen Institute’s head of data and technology. “So you have to bring the community together in order to understand it.”

There’s an urgent need to better prevent, diagnose and treat neurological conditions. The number of people worldwide living with or dying from conditions like stroke, Alzheimer’s disease and other dementias, and meningitis has increased significantly over recent decades, according to the Institute for Health Metrics and Evaluation.

In 2021, an estimated 3.4 billion people experienced a nervous system condition, which also includes brain injuries and migraines.

To create the Brain Knowledge Platform, the Allen Institute recruited participants to voluntarily share their data. Contributors include the Allen Institute for Brain Science, the Michael J. Fox Foundation for Parkinson’s Research, teams at the University of Washington and Harvard University, the Seattle Alzheimer’s Disease Brain Cell Atlas, or SEA-AD, and others.

Amazon Web Services engineered the tool’s core computing infrastructure while Google developed AI models for the neuroscience. Funding came from the Allen Institute as well as the National Institutes of Health’s Brain Research Through Advancing Innovative Neurotechnologies Initiative, or BRAIN Initiative.

Mufti said the resource is designed to be a “discovery platform,” not a traditional research tool where a scientist has a clear idea of what they are looking for. “How you can get to the ‘aha moments’ so you find something unexpected?” he asked.

Using the platform, scientists will be able to look across diseases. Studying the differences and similarities between people diagnosed with Alzheimer’s or Parkinson’s, for example, was previously laborious to make the data comparable.

With the Brain Knowledge Platform, “you can literally line those up side by side in the tool,” said Tyler Mollenkopf, associate director of data and technology at the Allen Institute.

While much of the data comes from research animals, information gathered from human brains — including 84 postmortem donors — is also available, stripped from identifying details.

The resource is offered to scientists for free. The team hopes more organizations contribute data and they’re devising a mechanism to provide attribution to credit researchers for their information, which could encourage sharing.

Given the massive societal impact of brain diseases “a real breakthrough is needed” to better understand them, said Mufti. “Let’s bring all the information together and make it discoverable. I’m hoping that [we] can really move the ball forward in a single community.”

Award-winning immunologist ​​Susan Kaech is the new executive vice president of the Allen Institute’s Immunology Moonshot, an initiative that aims to understand the immune system’s role in human health and disease.

Kaech currently leads the NOMIS Center for Immunobiology and Microbial Pathogenesis at the Salk Institute for Biological Studies and will join the Allen Institute in January.

“The appointment comes at a critical time in bioscience when the immune system is regarded as the cornerstone of all diseases and understanding its foundational principles is vital to unlocking new treatments and therapies,” the institute said in a statement.

Kaech’s research includes the investigation of how the immune system remembers infections to develop immunity, T-cell communications, and the role of metabolism in the immune system’s fight against cancer.

—  Seattle RFID company Impinj named Arthur Valdez Jr. to its board of directors.

Valdez recently left the role of executive VP of global supply chain and customer solutions at Starbucks and his career includes leadership roles at Amazon, Target and elsewhere.

“Arthur’s expertise transforming and optimizing strategic supply chain and logistics networks for large consumer-facing companies will be invaluable as we continue to advance our vision of connecting every thing,” said Impinj CEO Chris Diorio in a statement.

— Jason Bennett has taken a new role at Amazon Web Services, shifting from VP of U.S. enterprise to VP of worldwide startups and venture capital. Bennett has been with the company for more than 17 years.

On LinkedIn Bennett shared his fondness for working with startups and said he was eager to return to a position serving that community.

“I’m energized by the opportunity to work alongside our teams to support a thriving startup ecosystem — from founders and VCs, to accelerators, and the broader innovation community,” he said, adding that the work “has a lasting impact on the direction of industries and the future of AI.”

— NuScale Power named James Canafax as chief legal officer and corporate secretary. The Tigard, Ore.-based nuclear energy company is developing small modular reactors.

Canafax has decades of legal experience and joins NuScale from Maritime Partners. Past positions include executive leadership at BWX Technologies, which supplies nuclear components and services.

“[Canafax’s] extensive experience in the nuclear industry, deep familiarity with the regulatory environment and track record of guiding organizations through key growth periods make him uniquely suited to support NuScale at this important moment for our company,” CEO John Hopkins said in statement.

— Seattle entrepreneur Elvis Dieguez is now VP of data science, analytics and platforms for the healthcare startup hims & hers. Diegeuz joins the company from symphonie, a Seattle e-commerce marketing platform where he was CEO and co-founder. He was previously at Amazon for more than four years working in business analytics and as a senior manager.

Hims & hers offers a telehealth platform for conditions including sexual health, hair loss, mental health, skincare and weight loss.

“I look forward to leading and working with a ~70 person team who’ve been working hard to make the #healthcare system work for all Americans,” Dieguez said on LinkedIn.

— Biotech startup Synthesize Bio named Ariel Brumbaugh as senior director of business development. In the role, Brumbaugh will help the company partner with biopharma companies interested in using Synthesize’s AI-based research platform to accelerate and de-risk drug development.

Seattle’s Synthesize Bio was founded by leaders from Fred Hutchinson Cancer Center. Last month it announced $10 million in funding from Madrona.

Brumbaugh joined the startup from the San Francisco biotech company Gladstone Institutes.

— Sophie Brougham is director of philanthropic operations for the recently launched Clean Economy Project. Nicknamed CleanEcon, the effort includes past employees of the Bill Gates-led Breakthrough Energy and is a policy and advocacy platform promoting clean power.

Prior to Breakthrough, Brougham was with the Paul Allen holding company Vulcan (now known as Vale Group) for more than a decade, where she was a senior manager and led programs including philanthropic and grants management.

— Seattle’s Jake Laes is now executive director of AI Tinkerers, a global network of AI engineers and builders. Laes joined the group from Deel, where he helped facilitate partnerships between investors and accelerator programs. Laes is the founder of YoungTech Seattle, and his background includes mentoring and leadership roles at the University of Washington’s CoMotion and Techstars.

— Pranam Kolari, VP of search and recommendations at Coupang, is resigning from his role next month. Coupang is South Korea’s largest e-commerce platform and is headquartered in Seattle. Kolari, based in San Jose, Calif., was previously at Walmart Labs for nearly a decade where his roles included vice president of engineering for search.

— Datavault AI appointed Pete Scobell as VP of global security. The Beaverton, Ore.-based company helps businesses monetize their data and create digital twins of physical objects. Scobell is a decorated U.S. Navy SEAL veteran and will oversee Datavault AI’s security operations, risk management and asset logistics.

— Erin McHugh Saif, a former Massachusetts-based Microsoft executive, is CEO of an as-yet unnamed data and AI venture to serve “place-based partnerships,” which are networks of nonprofits, government agencies, and educational entities that aim to address education, jobs and housing needs.

“With better access to data, these organizations will leap ahead in this moment of AI transformation, gaining faster insight into which programs deliver the greatest improvement to significantly scale their impact,” Saif said on LinkedIn.

The effort has the support of the Ballmer Group, a philanthropic organization co-founded by former Microsoft CEO Steve Ballmer and his wife Connie, and the nonprofit TechSoup.

— Karen Ng was promoted to executive VP of product at HubSpot. Ng has been with the company since 2022, joining as senior VP of product and partnerships. Past employers include Common Room, Google and Microsoft, where she was chief of staff across the company’s developer tools business. Ng is based in the Seattle area.