In Vivo Data
in vivo data
Anton Arkhipov
The Scientist will develop bio-realistic network simulations at the level of a cortical area and the whole cortex, leveraging our multimodal datasets on brain composition and connectivity and training models on in vivo data using AI approaches. The goal is to use modeling together with experiments from our collaborators to understand the mechanisms underlying brain responses to sensory stimulation, including periodic sensory stimuli and the resulting entrainment of neuronal populations.
Learning and Memory
This webinar on learning and memory features three experts—Nicolas Brunel, Ashok Litwin-Kumar, and Julijana Gjorgieva—who present theoretical and computational approaches to understanding how neural circuits acquire and store information across different scales. Brunel discusses calcium-based plasticity and how standard “Hebbian-like” plasticity rules inferred from in vitro or in vivo datasets constrain synaptic dynamics, aligning with classical observations (e.g., STDP) and explaining how synaptic connectivity shapes memory. Litwin-Kumar explores insights from the fruit fly connectome, emphasizing how the mushroom body—a key site for associative learning—implements a high-dimensional, random representation of sensory features. Convergent dopaminergic inputs gate plasticity, reflecting a high-dimensional “critic” that refines behavior. Feedback loops within the mushroom body further reveal sophisticated interactions between learning signals and action selection. Gjorgieva examines how activity-dependent plasticity rules shape circuitry from the subcellular (e.g., synaptic clustering on dendrites) to the cortical network level. She demonstrates how spontaneous activity during development, Hebbian competition, and inhibitory-excitatory balance collectively establish connectivity motifs responsible for key computations such as response normalization.
Kilosort
Kilosort is a spike sorting pipeline for large-scale electrophysiology. Advances in silicon probe technology mean that in vivo electrophysiological recordings from hundreds of channels will soon become commonplace. To interpret these recordings we need fast, scalable and accurate methods for spike sorting, whose output requires minimal time for manual curation. Kilosort is a spike sorting framework that meets these criteria, and show that it allows rapid and accurate sorting of large-scale in vivo data. Kilosort models the recorded voltage as a sum of template waveforms triggered on the spike times, allowing overlapping spikes to be identified and resolved. Rapid processing is achieved thanks to a novel low-dimensional approximation for the spatiotemporal distribution of each template, and to batch-based optimization on GPUs. Kilosort is an important step towards fully automated spike sorting of multichannel electrode recordings, and is freely available.
Hebbian learning, its inference, and brain oscillation
Despite the recent success of deep learning in artificial intelligence, the lack of biological plausibility and labeled data in natural learning still poses a challenge in understanding biological learning. At the other extreme lies Hebbian learning, the simplest local and unsupervised one, yet considered to be computationally less efficient. In this talk, I would introduce a novel method to infer the form of Hebbian learning from in vivo data. Applying the method to the data obtained from the monkey inferior temporal cortex for the recognition task indicates how Hebbian learning changes the dynamic properties of the circuits and may promote brain oscillation. Notably, recent electrophysiological data observed in rodent V1 showed that the effect of visual experience on direction selectivity was similar to that observed in monkey data and provided strong validation of asymmetric changes of feedforward and recurrent synaptic strengths inferred from monkey data. This may suggest a general learning principle underlying the same computation, such as familiarity detection across different features represented in different brain regions.