Tag: Allen Institute

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Scientists simulate the brain on a supercomputer

Visuaization of mouse cortex
This color-coded representation of a mouse cortex simulates the activity of brain cells. (Video via Allen Institute)

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.

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Scientists enlist AI to map regions of the brain in detail

Illustration: Color-coded cutaway view of mouse brain
An AI-produced rendering shows a map of mouse brain regions, overlaid with network motifs. (UCSF Illustration)

Scientists say an artificial intelligence program that they compare to ChatGPT has helped them create one of the most detailed maps of the mouse brain to date, with 1,300 regions and subregions marked on the map.

Some of those subregions have never been charted before — and the researchers say there’s more to come. “I think there are already indications that we can go beyond what we see now,” said Bosiljka Tasic, director of molecular genetics at Seattle’s Allen Institute for Brain Science.

The mapping effort, led by researchers at the University of California at San Francisco and the Allen Institute, is detailed in a study published today in the journal Nature Communications.

“Our model is built on the same powerful technology as AI tools like ChatGPT,” senior author Reza Abbasi-Asl, a neuroscientist at UCSF, said in a news release. “Both are built on a ‘transformer’ network which excels at understanding context.”

That context could be important for treating neurological ailments, Tasic told me. “Location is everything in the brain,” she said. “Defining the geography of the brain, and then defining all these regions and their functions, not only leads to better understanding, but also better ability to treat.”

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Scientists study the brain cells that show us illusions

Jerome Lecoq points to diagram on computer screen
Neuroscientist Jerome Lecoq points to a diagram that was used to study how the brain interprets illusions. (Allen Institute Photo / Erik Dinnel)

Our brains are wired to fill in perceptual gaps in what we see, whether it’s a lion hiding in the trees or the shapes hidden in an optical illusion — but how does that wiring work? Neuroscientists are zeroing in on how special kinds of brain cells help us see things that aren’t actually there.

Researchers from Seattle’s Allen Institute for Brain Science and the University of California at Berkeley traced the role played by the cells, known as IC-encoder neurons, in a study published today by the journal Nature Neuroscience.

“The goal of this project was to understand the neural basis of pattern completion, or filling in when you are dealt ambiguous or missing data in your vision,” said senior study author Hillel Adesnik, a neuroscientist at Berkeley.

Such research could help scientists understand how our brains create a complete picture of the world around us from the data that our senses provide. It could also eventually reveal how hallucinations arise, or point the way to better computer vision systems.

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Scientists create new toolkit to fight brain diseases

Color-coded images of mouse brain cell populations
This graphic shows different populations of mouse brain cells, each one targeted by a tool in a new genetic toolkit. (Allen Institute Graphic)

Scientists say they’ve put together a new kind of molecular toolkit that could eventually be used to treat a variety of brain diseases, possibly including epilepsy, sleep disorders and Huntington’s disease.

The kit currently contains more than 1,000 tools of a type known as enhancer AAV vectors, with AAV standing for “adeno-associated virus.” A consortium that included researchers from Seattle’s Allen Institute for Brain Science and the University of Washington combined harmless adeno-associated viruses with snippets of engineered DNA to create a gene-therapy package that could target specific neurons in the brain while having no effect on other cells.

Researchers laid out their findings in a set of eight studies published today in the Cell Press family of journals. The work is part of a project called the Armamentarium for Precision Brain Cell Access, funded through the National Institutes of Health’s BRAIN Initiative.

“Honing in on the right cells — in the right way and at the right time — is the future of precision brain medicine,” John Ngai, director of the BRAIN Initiative, said in a news release. “These tools move us closer to that future, while also expanding what we know about the brain’s cells and circuits today.”

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New clues in the search for the roots of consciousness

Map of the brain, plus charts of brain activity
This map of the human brain highlights areas in the prefrontal cortex (green) and the visual cortex (blue) that are thought to be associated with consciousness. The graphs track readings of brain activity. (Adapted from Cogitate Consortium Graphic / Melloni et al. / Nature)

Seven years after they started, neuroscientists have published the results of a landmark study that was designed to determine which theory of human consciousness came closest to the mark — and those results are decidedly mixed.

The bad news is that neither of the leading theories held a clear advantage in explaining how consciousness arises. The good news is that researchers picked up new clues about where to look.

One of the leaders of the effort — Christof Koch, a meritorious investigator at the Seattle-based Allen Institute — said he was heartened by the state of the debate.

“Adversarial collaboration fits within the Allen Institute’s mission of team science, open science and big science, in service of one of the biggest, and most long-standing, intellectual challenges of humanity: the Mind-Body Problem,” Koch said in a news release. “Unraveling this mystery is the passion of my entire life.”

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AI experts look ahead to artificial general intelligence

Sophia the Robot
A robot named Sophia can carry on a conversation and make facial expressions. (Hanson Robotics Photo)

There’s no question that artificial intelligence is rapidly becoming more intelligent, thanks to software platforms including ChatGPT, Google Gemini and Grok. But does that mean AI agents will one day outdo the generalized smarts that distinguish human intelligence? And if so, is that good or bad for humanity? Those were just a couple of the questions raised during this week’s AGI-24 conference in Seattle.

Conference sessions at the University of Washington centered on a concept known as artificial general intelligence, or AGI. Artificial intelligence can already outperform humans on a growing list of specialized tasks, ranging from playing the game of Go to diagnosing some forms of cancer. But humans are still more intelligent than AI agents when it comes to dealing with a wider range of tasks, including tasks they haven’t been trained to do. That’s what AGI is all about.

David Hanson, a roboticist and artist who’s best known for creating a humanoid robot named Sophia, said the questions surrounding human-level intelligence and consciousness are a high priority for his team at Hanson Robotics.

“The goal really is continuously to explore what it means to be intelligent,” he said during an Aug. 16 session. “How can we achieve consciousness? How can we make machines that co-evolve with humans? All of these efforts, while they’re really cool, and I’m very proud of them, they’re all just trying to get the engine to start on this kind of conscious machine that can co-evolve with humans.”

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How a brainstorm could unlock mysteries of the mind

Jerome Lecoq in Allen Brain Observatory's lab
Allen Institute researcher Jerome Lecoq sets up a microscope in the Allen Brain Observatory. (Allen Institute Photo)

The Allen Institute’s OpenScope program lets scientists study the weird workings of the brain — for instance, how magic mushrooms work their psychedelic magic on neurons, how memories of the past influence perceptions of the present, and how the brain’s visual system interprets motion and texture.

But one of the program’s leaders, neuroscientist Jerome Lecoq, says he’s really excited about an experiment that hasn’t yet been fully defined. It’s a study that could support a theory about the mechanism by which sensory data is fed into our consciousness — to modify our view of the world, and perhaps to modify our behavior as well.

The experiment is being fine-tuned online by an international community of researchers, through an open-source process that the Seattle-based Allen Institute fittingly calls a “brainstorm.”

“You can just go and follow us on Twitter and visit the Google Doc,” Lecoq says in the latest episode of the Fiction Science podcast. “We’re going to meet in two weeks and a half in Boston at a conference and discuss this experiment. The document is very open. If you have a good idea, please chime in.”

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Scientists unveil complete cell atlas for mouse brain

Mandala combining visualizations of cell distribution in mouse brain
This mandala combines visualizations of cell types in the mouse brain. (Illustration via Allen Institute)

Neuroscientists have unveiled their most comprehensive and detailed map of cell types across the entire mouse brain, delivering the latest results of a six-year-long scientific effort in which Seattle’s Allen Institute has played a leading role.

Nine studies published today in the journal Nature document the identification of 5,322 different types of brain cells, and trace the similarities and differences found in a variety of mammalian species — including humans.

The work expands upon previous studies from the BRAIN Initiative Cell Census Network, including earlier surveys of cells in various regions of the mouse brain, as well as cross-species comparisons of cell functions. Researchers from the Allen Institute joined forces with colleagues from the Broad Institute, Harvard, the Salk Institute for Biological Studies, the University of California at San Diego, UC-Berkeley and other institutions to add to their “parts list” for the brain.

“Now we have the cell-type atlas of all the cells in the brain,” Hongkui Zeng, executive vice president and director of the Allen Institute for Brain Science, said in an explanatory video. “This is really a landmark achievement. … It marks the completion of a kind of work that strives for completeness. But it also marks the beginning of the next phase of the journey. It just opens up the door for the next generation of investigations.”

Zeng, who is the senior author of one of the papers in Nature and a co-author of five others, said the next step will be to figure out exactly what all those different cell types do, how their functions are affected by disease, and whether there might be yet-to-be-discovered ways to restore those proper functions.

“It’s not just about a catalog, a list of cell types and where they are — reference information which by itself is already important — but we begin to see how a brain is organized,” Zeng said.

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Scientists team up to turn cells into tiny recording devices

Cell lineage map
A small section of a cell lineage map produced using DNA Typewriter. (Allen Institute / UW Image)

The Allen Institute, the Chan Zuckerberg Initiative and the University of Washington have launched a collaboration called the Seattle Hub for Synthetic Biology, with the goal of using genetically modified cells to capture a DNA-based record showing how they change over time.

If the project works out as hoped, it could lead to a deeper understanding of the mechanisms behind cellular processes — including, for example, how tumors grow — and point to new methods for fighting disease and promoting healthy cell growth.

Over the next five years, the Seattle Hub for Synthetic Biology will receive $35 million from the Allen Institute, and another $35 million from the Chan Zuckerberg Initiative, founded by Meta CEO Mark Zuckerberg and his wife, Priscilla Chan.

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Allen Frontiers Group awards $10M for neuroimmunology

Immune cells in spinal cord region
Immune cells (yellow and purple) fill a sinus (teal) in the outer layer of the meninges, the tissue that surrounds the brain and spinal cord. (Credit: Justin Rustenhoven / Washington University School of Medicine in St. Louis)

The Paul G. Allen Frontiers Group, a division of the Seattle-based Allen Institute, is launching a research center in New York to focus on interactions between the nervous system and the immune system.

The Allen Discovery Center for Neuroimmune Interactions, headquartered at the Icahn School of Medicine at Mount Sinai, will receive $10 million over the course of four years from the Paul G. Allen Family Foundation, with a total potential for $20 million over eight years.

The award is the result of an open call for research proposals exploring fundamental questions at the intersection of neuroscience and immunology. It’s the latest open-science initiative celebrating the legacy of Microsoft co-founder Paul Allen, who died five years ago at the age of 65 from complications of non-Hodgkin’s lymphoma.

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