Brain Inspired – Details, episodes & analysis

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The Transmitter is an online publication that aims to deliver useful information, insights and tools to build bridges across neuroscience and advance research. Visit thetransmitter.org to explore the latest neuroscience news and perspectives, written by journalists and scientists.

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What changes and what stays the same as you scale from single neurons up to local populations of neurons up to whole brains? How tuning parameters like the gain in some neural populations affects the dynamical and computational properties of the rest of the system.

Those are the main questions my guests today discuss. Michael Breakspear is a professor of Systems Neuroscience and runs the Systems Neuroscience Group at the University of Newcastle in Australia. Mac Shine is back, he was here a few years ago. Mac runs the Shine Lab at the University of Sidney in Australia.

Michael and Mac have been collaborating on the questions I mentioned above, using a systems approach to studying brains and cognition. The short summary of what they discovered in their first collaboration is that turning up or down the gain across broad networks of neurons in the brain affects integration - working together - and segregation - working apart. They map this gain modulation on to the ascending arousal pathway, in which the locus coeruleus projects widely throughout the brain distributing noradrenaline. At a certain sweet spot of gain, integration and segregation are balanced near a bifurcation point, near criticality, which maximizes properties that are good for cognition.

In their recent collaboration, they used a coarse graining procedure inspired by physics to study the collective dynamics of various sizes of neural populations, going from single neurons to large populations of neurons. Here they found that despite different coding properties at different scales, there are also scale-free properties that suggest neural populations of all sizes, from single neurons to brains, can do cognitive stuff useful for the organism. And they found this is a conserved property across many different species, suggesting it's a universal principle of brain dynamics in general.

So we discuss all that, but to get there we talk about what a systems approach to neuroscience is, how systems neuroscience has changed over the years, and how it has inspired the questions Michael and Mac ask.

• Breakspear: Systems Neuroscience Group.
  • @DrBreaky.
• Shine: Shine Lab.
  • @jmacshine.
• Related papers
  • Dynamic models of large-scale brain activity
  • Metastable brain waves
  • The modulation of neural gain facilitates a transition between functional segregation and integration in the brain
  • Multiscale Organization of Neuronal Activity Unifies Scale-Dependent Theories of Brain Function.
  • The brain that controls itself.
  • Metastability demystified — the foundational past, the pragmatic present and the promising future.
  • Generation of surrogate brain maps preserving spatial autocorrelation through random rotation of geometric eigenmodes.
• Related episodes
  • BI 212 John Beggs: Why Brains Seek the Edge of Chaos
  • BI 216 Woodrow Shew and Keith Hengen: The Nature of Brain Criticality
  • BI 121 Mac Shine: Systems Neurobiology

Read the transcript.

0:00 - Intro 4:28 - Neuroscience vs neurobiology 8:01 - Systems approach 26:52 - Physics for neuroscience 33:15 - Gain and bifurcation: earliest collaboration 55:32 - Multiscale organization 1:17:54 - Roadblocks

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The Transmitter is an online publication that aims to deliver useful information, insights and tools to build bridges across neuroscience and advance research. Visit thetransmitter.org to explore the latest neuroscience news and perspectives, written by journalists and scientists.

Read more about our partnership.

Sign up for Brain Inspired email alerts to be notified every time a new Brain Inspired episode is released.

To explore more neuroscience news and perspectives, visit thetransmitter.org.

Xaq Pitkow runs the Lab for the Algorithmic Brain at Carnegie Mellon University. The main theme of our discussion is how Xaq approaches his research into cognition by way of principles, from which his questions and models and methods spring forth. We discuss those principles, and In that light, we discuss some of his specific lines of work and ideas on the theoretical side of trying understand and explain a slew of cognitive processes. A few of the specifics we discuss are:

• How when we present tasks for organisms to solve, they use strategies that are suboptimal relative to the task, but nearly optimal relative to their beliefs about what they need to do - something Xaq calls inverse rational control.
• Probabilistic graph networks.
• How brains use probabilities to compute.
• A new ecological neuroscience project Xaq has started with multiple collaborators.

• LAB: Lab for the Algorithmic Brain.
• Related papers
  • How does the brain compute with probabilities?
  • Rational thoughts in neural codes.
  • Control when confidence is costly
  • Generalization of graph network inferences in higher-order graphical models.
  • Attention when you need.

Read the transcript.

0:00 - Intro 3:57 - Xaq's approach 8:28 - Inverse rational control 19:19 - Space of input-output functions 24:48 - Cognition for cognition 27:35 - Theory vs. experiment 40:32 - How does the brain compute with probabilities? 1:03:57 - Normative vs kludge 1:07:44 - Ecological neuroscience 1:20:47 - Representations 1:29:34 - Current projects 1:36:04 - Need a synaptome 1:42:20 - Across scales

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Dean Buonomano runs the Buonomano lab at UCLA. Dean was a guest on Brain Inspired way back on episode 18, where we talked about his book Your Brain is a Time Machine: The Neuroscience and Physics of Time, which details much of his thought and research about how centrally important time is for virtually everything we do, different conceptions of time in philosophy, and how how brains might tell time. That was almost 7 years ago, and his work on time and dynamics in computational neuroscience continues.

One thing we discuss today, later in the episode, is his recent work using organotypic brain slices to test the idea that cortical circuits implement timing as a computational primitive it's something they do by they're very nature. Organotypic brain slices are between what I think of as traditional brain slices and full on organoids. Brain slices are extracted from an organism, and maintained in a brain-like fluid while you perform experiments on them. Organoids start with a small amount of cells that you the culture, and let them divide and grow and specialize, until you have a mass of cells that have grown into an organ of some sort, to then perform experiments on. Organotypic brain slices are extracted from an organism, like brain slices, but then also cultured for some time to let them settle back into some sort of near-homeostatic point - to them as close as you can to what they're like in the intact brain... then perform experiments on them. Dean and his colleagues use optigenetics to train their brain slices to predict the timing of the stimuli, and they find the populations of neurons do indeed learn to predict the timing of the stimuli, and that they exhibit replaying of those sequences similar to the replay seen in brain areas like the hippocampus.

But, we begin our conversation talking about Dean's recent piece in The Transmitter, that I'll point to in the show notes, called The brain holds no exclusive rights on how to create intelligence. There he argues that modern AI is likely to continue its recent successes despite the ongoing divergence between AI and neuroscience. This is in contrast to what folks in NeuroAI believe.

We then talk about his recent chapter with physicist Carlo Rovelli, titled Bridging the neuroscience and physics of time, in which Dean and Carlo examine where neuroscience and physics disagree and where they agree about the nature of time.

Finally, we discuss Dean's thoughts on the integrated information theory of consciousness, or IIT. IIT has see a little controversy lately. Over 100 scientists, a large part of that group calling themselves IIT-Concerned, have expressed concern that IIT is actually unscientific. This has cause backlash and anti-backlash, and all sorts of fun expression from many interested people. Dean explains his own views about why he thinks IIT is not in the purview of science - namely that it doesn't play well with the existing ontology of what physics says about science. What I just said doesn't do justice to his arguments, which he articulates much better.

• Buonomano lab.
• Twitter: @DeanBuono.
• Related papers
  • The brain holds no exclusive rights on how to create intelligence.
  • What makes a theory of consciousness unscientific?
  • Ex vivo cortical circuits learn to predict and spontaneously replay temporal patterns.
  • Bridging the neuroscience and physics of time.
• BI 204 David Robbe: Your Brain Doesn’t Measure Time

Read the transcript.

0:00 - Intro 8:49 - AI doesn't need biology 17:52 - Time in physics and in neuroscience 34:04 - Integrated information theory 1:01:34 - Global neuronal workspace theory 1:07:46 - Organotypic slices and predictive processing 1:26:07 - Do brains actually measure time? David Robbe

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Mac and I discuss his systems level approach to understanding brains, and his theoretical work suggesting important roles for the thalamus, basal ganglia, and cerebellum, shifting the dynamical landscape of brain function within varying behavioral contexts. We also discuss his recent interest in the ascending arousal system and neuromodulators. Mac thinks the neocortex has been the sole focus of too much neuroscience research, and that the subcortical brain regions and circuits have a much larger role underlying our intelligence.

• Shine Lab
• Twitter: @jmacshine
• Related papers
  • The thalamus integrates the macrosystems of the brain to facilitate complex, adaptive brain network dynamics.
  • Computational models link cellular mechanisms of neuromodulation to large-scale neural dynamics.

0:00 - Intro 6:32 - Background 10:41 - Holistic approach 18:19 - Importance of thalamus 35:19 - Thalamus circuitry 40:30 - Cerebellum 46:15 - Predictive processing 49:32 - Brain as dynamical attractor landscape 56:48 - System 1 and system 2 1:02:38 - How to think about the thalamus 1:06:45 - Causality in complex systems 1:11:09 - Clinical applications 1:15:02 - Ascending arousal system and neuromodulators 1:27:48 - Implications for AI 1:33:40 - Career serendipity 1:35:12 - Advice

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James, Andrew, and Weinan discuss their recent theory about how the brain might use complementary learning systems to optimize our memories. The idea is that our hippocampus creates our episodic memories for individual events, full of particular details. And through a complementary process, slowly consolidates those memories within our neocortex through mechanisms like hippocampal replay. The new idea in their work suggests a way for the consolidated cortical memory to become optimized for generalization, something humans are known to be capable of but deep learning has yet to build. We discuss what their theory predicts about how the "correct" process depends on how much noise and variability there is in the learning environment, how their model solves this, and how it relates to our brain and behavior.

• James' Janelia page.
• Weinan's Janelia page.
• Andrew's website.
• Twitter:
  • Andrew: @SaxeLab
  • Weinan: @sunw37
• Paper we discuss:
  • Organizing memories for generalization in complementary learning systems.
• Andrew's previous episode: BI 052 Andrew Saxe: Deep Learning Theory

0:00 - Intro 3:57 - Guest Intros 15:04 - Organizing memories for generalization 26:48 - Teacher, student, and notebook models 30:51 - Shallow linear networks 33:17 - How to optimize generalization 47:05 - Replay as a generalization regulator 54:57 - Whole greater than sum of its parts 1:05:37 - Unpredictability 1:10:41 - Heuristics 1:13:52 - Theoretical neuroscience for AI 1:29:42 - Current personal thinking

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Henry and I discuss why he thinks neuroscience is in a crisis (in the Thomas Kuhn sense of scientific paradigms, crises, and revolutions). Henry thinks our current concept of the brain as an input-output device, with cognition in the middle, is mistaken. He points to the failure of neuroscience to successfully explain behavior despite decades of research. Instead, Henry proposes the brain is one big hierarchical set of control loops, trying to control their output with respect to internally generated reference signals. He was inspired by control theory, but points out that most control theory for biology is flawed by not recognizing that the reference signals are internally generated. Instead, most control theory approaches, and neuroscience research in general, assume the reference signals are what gets externally supplied... by the experimenter.

• Yin lab at Duke.
• Twitter: @HenryYin19.
• Related papers
  • The Crisis in Neuroscience.
  • Restoring Purpose in Behavior.
  • Achieving natural behavior in a robot using neurally inspired hierarchical perceptual control.

0:00 - Intro 5:40 - Kuhnian crises 9:32 - Control theory and cybernetics 17:23 - How much of brain is control system? 20:33 - Higher order control representation 23:18 - Prediction and control theory 27:36 - The way forward 31:52 - Compatibility with mental representation 38:29 - Teleology 45:53 - The right number of subjects 51:30 - Continuous measurement 57:06 - Artificial intelligence and control theory

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Johannes (Yogi) is a freelance philosopher, researcher & educator. We discuss many of the topics in his online course, Beyond Networks: The Evolution of Living Systems. The course is focused on the role of agency in evolution, but it covers a vast range of topics: process vs. substance metaphysics, causality, mechanistic dynamic explanation, teleology, the important role of development mediating genotypes, phenotypes, and evolution, what makes biological organisms unique, the history of evolutionary theory, scientific perspectivism, and a view toward the necessity of including agency in evolutionary theory. I highly recommend taking his course. We also discuss the role of agency in artificial intelligence, how neuroscience and evolutionary theory are undergoing parallel re-evaluations, and Yogi answers a guest question from Kevin Mitchell.

• Yogi's website and blog: Untethered in the Platonic Realm.
• Twitter: @yoginho.
• His youtube course: Beyond Networks: The Evolution of Living Systems.
• Kevin Mitchell's previous episode: BI 111 Kevin Mitchell and Erik Hoel: Agency, Emergence, Consciousness.

0:00 - Intro 4:10 - Yogi's background 11:00 - Beyond Networks - limits of dynamical systems models 16:53 - Kevin Mitchell question 20:12 - Process metaphysics 26:13 - Agency in evolution 40:37 - Agent-environment interaction, open-endedness 45:30 - AI and agency 55:40 - Life and intelligence 59:08 - Deep learning and neuroscience 1:03:21 - Mental autonomy 1:06:10 - William Wimsatt's biopsychological thicket 1:11:23 - Limtiations of mechanistic dynamic explanation 1:18:53 - Synthesis versus multi-perspectivism 1:30:31 - Specialization versus generalization

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Anil and I discuss a range of topics from his book, BEING YOU A New Science of Consciousness. Anil lays out his framework for explaining consciousness, which is embedded in what he calls the "real problem" of consciousness. You know the "hard problem", which was David Chalmers term for our eternal difficulties to explain why we have subjective awareness at all instead of being unfeeling, unexperiencing machine-like organisms. Anil's "real problem" aims to explain, predict, and control the phenomenal properties of consciousness, and his hope is that, by doing so, the hard problem of consciousness will dissolve much like the mystery of explaining life dissolved with lots of good science.

Anil's account of perceptual consciousness, like seeing red, is that it's rooted in predicting our incoming sensory data. His account of our sense of self,  is that it's rooted in predicting our bodily states to control them.

We talk about that and a lot of other topics from the book, like consciousness as "controlled hallucinations", free will, psychedelics, complexity and emergence, and the relation between life, intelligence, and consciousness. Plus, Anil answers a handful of questions from Megan Peters and Steve Fleming, both previous brain inspired guests.

• Anil's website.
• Twitter: @anilkseth.
• Anil's book: BEING YOU A New Science of Consciousness.
• Megan's previous episode:
  • BI 073 Megan Peters: Consciousness and Metacognition
• Steve's previous episodes
  • BI 099 Hakwan Lau and Steve Fleming: Neuro-AI Consciousness
  • BI 107 Steve Fleming: Know Thyself

0:00 - Intro 6:32 - Megan Peters Q: Communicating Consciousness 15:58 - Human vs. animal consciousness 19:12 - BEING YOU A New Science of Consciousness 20:55 - Megan Peters Q: Will the hard problem go away? 30:55 - Steve Fleming Q: Contents of consciousness 41:01 - Megan Peters Q: Phenomenal character vs. content 43:46 - Megan Peters Q: Lempels of complexity 52:00 - Complex systems and emergence 55:53 - Psychedelics 1:06:04 - Free will 1:19:10 - Consciousness vs. life vs. intelligence

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Mike and I discuss his modeling approach to study cognition. Many people I have on the podcast use deep neural networks to study brains, where the idea is to train or optimize the model to perform a task, then compare the model properties with brain properties. Mike's approach is different in at least two ways. One, he builds the architecture of his models using connectivity data from fMRI recordings. Two, he doesn't train his models; instead, he uses functional connectivity data from the fMRI recordings to assign weights between nodes of the network (in deep learning, the weights are learned through lots of training). Mike calls his networks empirically-estimated neural networks (ENNs), and/or network coding models. We walk through his approach, what we can learn from models like ENNs, discuss some of his earlier work on cognitive control and our ability to flexibly adapt to new task rules through instruction, and he fields questions from Kanaka Rajan, Kendrick Kay, and Patryk Laurent.

• The Cole Neurocognition lab.
• Twitter: @TheColeLab.
• Related papers
  • Discovering the Computational Relevance of Brain Network Organization.
  • Constructing neural network models from brain data reveals representational transformation underlying adaptive behavior.
• Kendrick Kay's previous episode: BI 026 Kendrick Kay: A Model By Any Other Name.
• Kanaka Rajan's previous episode: BI 054 Kanaka Rajan: How Do We Switch Behaviors?

0:00 - Intro 4:58 - Cognitive control 7:44 - Rapid Instructed Task Learning and Flexible Hub Theory 15:53 - Patryk Laurent question: free will 26:21 - Kendrick Kay question: fMRI limitations 31:55 - Empirically-estimated neural networks (ENNs) 40:51 - ENNs vs. deep learning 45:30 - Clinical relevance of ENNs 47:32 - Kanaka Rajan question: a proposed collaboration 56:38 - Advantage of modeling multiple regions 1:05:30 - How ENNs work 1:12:48 - How ENNs might benefit artificial intelligence 1:19:04 - The need for causality 1:24:38 - Importance of luck and serendipity

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Steve and I discuss his book Conscious Mind, Resonant Brain: How Each Brain Makes a Mind.  The book is a huge collection of his models and their predictions and explanations for a wide array of cognitive brain functions. Many of the models spring from his Adaptive Resonance Theory (ART) framework, which explains how networks of neurons deal with changing environments while maintaining self-organization and retaining learned knowledge. ART led Steve to the hypothesis that all conscious states are resonant states, which we discuss. There are also guest questions from György Buzsáki, Jay McClelland, and John Krakauer.

• Steve's BU website.
• Conscious Mind, Resonant Brain: How Each Brain Makes a Mind
• Previous Brain Inspired episode:
  • BI 082 Steve Grossberg: Adaptive Resonance Theory

0:00 - Intro 2:38 - Conscious Mind, Resonant Brain 11:49 - Theoretical method 15:54 - ART, learning, and consciousness 22:58 - Conscious vs. unconscious resonance 26:56 - Györy Buzsáki question 30:04 - Remaining mysteries in visual system 35:16 - John Krakauer question 39:12 - Jay McClelland question 51:34 - Any missing principles to explain human cognition? 1:00:16 - Importance of an early good career start 1:06:50 - Has modeling training caught up to experiment training? 1:17:12 - Universal development code