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1. Continual Learning with Deep Artificial Neurons

   Camp, Brendan; Mandivarapu, Jaya K.; Estrada, Rolando (April 2022, International Conference on Learning Representations (ICLR) Workshop: From Cells to Societies)

   Neurons in real brains are complex computational units, capable of input-specific damping, inter-trial memory, and context-dependent signal processing. Artificial neurons, on the other hand, are usually implemented as simple weighted sums. Here we explore if increasing the computational power of individual neurons can yield more powerful neural networks. Specifically, we introduce Deep Artificial Neurons (DANs)—small neural networks with shared, learnable parameters embedded within a larger network. DANs act as filters between nodes in the net-work; namely, they receive vectorized inputs from multiple neurons in the previous layer, condense these signals into a single output, then send this processed signal to the neurons in the subsequent layer. We demonstrate that it is possible to meta-learn shared parameters for the various DANS in the network in order to facilitate continual and transfer learning during deployment. Specifically, we present experimental results on (1) incremental non-linear regression tasks and (2)unsupervised class-incremental image reconstruction that show that DANs allow a single network to update its synapses (i.e., regular weights) over time with minimal forgetting. Notably, our approach uses standard backpropagation, does not require experience replay, and does need separate wake/sleep phases. 

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2. The connectome of an insect brain

   https://doi.org/10.1126/science.add9330  

   Winding, Michael; Pedigo, Benjamin D.; Barnes, Christopher L.; Patsolic, Heather G.; Park, Youngser; Kazimiers, Tom; Fushiki, Akira; Andrade, Ingrid V.; Khandelwal, Avinash; Valdes-Aleman, Javier; et al (March 2023, Science)

   INTRODUCTION A brainwide, synaptic-resolution connectivity map—a connectome—is essential for understanding how the brain generates behavior. However because of technological constraints imaging entire brains with electron microscopy (EM) and reconstructing circuits from such datasets has been challenging. To date, complete connectomes have been mapped for only three organisms, each with several hundred brain neurons: the nematode C. elegans , the larva of the sea squirt Ciona intestinalis , and of the marine annelid Platynereis dumerilii . Synapse-resolution circuit diagrams of larger brains, such as insects, fish, and mammals, have been approached by considering select subregions in isolation. However, neural computations span spatially dispersed but interconnected brain regions, and understanding any one computation requires the complete brain connectome with all its inputs and outputs. RATIONALE We therefore generated a connectome of an entire brain of a small insect, the larva of the fruit fly, Drosophila melanogaster. This animal displays a rich behavioral repertoire, including learning, value computation, and action selection, and shares homologous brain structures with adult Drosophila and larger insects. Powerful genetic tools are available for selective manipulation or recording of individual neuron types. In this tractable model system, hypotheses about the functional roles of specific neurons and circuit motifs revealed by the connectome can therefore be readily tested. RESULTS The complete synaptic-resolution connectome of the Drosophila larval brain comprises 3016 neurons and 548,000 synapses. We performed a detailed analysis of the brain circuit architecture, including connection and neuron types, network hubs, and circuit motifs. Most of the brain’s in-out hubs (73%) were postsynaptic to the learning center or presynaptic to the dopaminergic neurons that drive learning. We used graph spectral embedding to hierarchically cluster neurons based on synaptic connectivity into 93 neuron types, which were internally consistent based on other features, such as morphology and function. We developed an algorithm to track brainwide signal propagation across polysynaptic pathways and analyzed feedforward (from sensory to output) and feedback pathways, multisensory integration, and cross-hemisphere interactions. We found extensive multisensory integration throughout the brain and multiple interconnected pathways of varying depths from sensory neurons to output neurons forming a distributed processing network. The brain had a highly recurrent architecture, with 41% of neurons receiving long-range recurrent input. However, recurrence was not evenly distributed and was especially high in areas implicated in learning and action selection. Dopaminergic neurons that drive learning are amongst the most recurrent neurons in the brain. Many contralateral neurons, which projected across brain hemispheres, were in-out hubs and synapsed onto each other, facilitating extensive interhemispheric communication. We also analyzed interactions between the brain and nerve cord. We found that descending neurons targeted a small fraction of premotor elements that could play important roles in switching between locomotor states. A subset of descending neurons targeted low-order post-sensory interneurons likely modulating sensory processing. CONCLUSION The complete brain connectome of the Drosophila larva will be a lasting reference study, providing a basis for a multitude of theoretical and experimental studies of brain function. The approach and computational tools generated in this study will facilitate the analysis of future connectomes. Although the details of brain organization differ across the animal kingdom, many circuit architectures are conserved. As more brain connectomes of other organisms are mapped in the future, comparisons between them will reveal both common and therefore potentially optimal circuit architectures, as well as the idiosyncratic ones that underlie behavioral differences between organisms. Some of the architectural features observed in the Drosophila larval brain, including multilayer shortcuts and prominent nested recurrent loops, are found in state-of-the-art artificial neural networks, where they can compensate for a lack of network depth and support arbitrary, task-dependent computations. Such features could therefore increase the brain’s computational capacity, overcoming physiological constraints on the number of neurons. Future analysis of similarities and differences between brains and artificial neural networks may help in understanding brain computational principles and perhaps inspire new machine learning architectures. The connectome of the Drosophila larval brain. The morphologies of all brain neurons, reconstructed from a synapse-resolution EM volume, and the synaptic connectivity matrix of an entire brain. This connectivity information was used to hierarchically cluster all brains into 93 cell types, which were internally consistent based on morphology and known function. 

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3. Pathway-like Activation of 3D Neuronal Constructs with an Optical Interface

   https://doi.org/10.3390/bios15030179  

   Omidi, Saeed; Berdichevsky, Yevgeny (March 2025, Biosensors)

   Three-dimensional neuronal organoids, spheroids, and tissue mimics are increasingly used to model cognitive processes in vitro. These 3D constructs are also used to model the effects of neurological and psychiatric disorders and to perform computational tasks. The brain’s complex network of neurons is activated via feedforward sensory pathways. Therefore, an interface to 3D constructs that models sensory pathway-like inputs is desirable. In this work, an optical interface for 3D neuronal constructs was developed. Dendrites and axons extended by cortical neurons within the 3D constructs were guided into microchannel-confined bundles. These neurite bundles were then optogenetically stimulated, and evoked responses were evaluated by calcium imaging. Optical stimulation was designed to deliver distinct input patterns to the network in the 3D construct, mimicking sensory pathway inputs to cortical areas in the intact brain. Responses of the network to the stimulation possessed features of neuronal population code, including separability by input pattern and mixed selectivity of individual neurons. This work represents the first demonstration of a pathway-like activation of networks in 3D constructs. Another innovation of this work is the development of an all-optical interface to 3D neuronal constructs, which does not require the use of expensive microelectrode arrays. This interface may enable the use of 3D neuronal constructs for investigations into cortical information processing. It may also enable studies into the effects of neurodegenerative or psychiatric disorders on cortical computation. 

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4. A developmental framework linking neurogenesis and circuit formation in the Drosophila CNS

   https://doi.org/10.7554/eLife.67510  

   Mark, Brandon; Lai, Sen-Lin; Zarin, Aref Arzan; Manning, Laurina; Pollington, Heather Q; Litwin-Kumar, Ashok; Cardona, Albert; Truman, James W; Doe, Chris Q (May 2021, eLife)

   null (Ed.)

   The mechanisms specifying neuronal diversity are well characterized, yet it remains unclear how or if these mechanisms regulate neural circuit assembly. To address this, we mapped the developmental origin of 160 interneurons from seven bilateral neural progenitors (neuroblasts) and identify them in a synapse-scale TEM reconstruction of the Drosophila larval central nervous system. We find that lineages concurrently build the sensory and motor neuropils by generating sensory and motor hemilineages in a Notch-dependent manner. Neurons in a hemilineage share common synaptic targeting within the neuropil, which is further refined based on neuronal temporal identity. Connectome analysis shows that hemilineage-temporal cohorts share common connectivity. Finally, we show that proximity alone cannot explain the observed connectivity structure, suggesting hemilineage/temporal identity confers an added layer of specificity. Thus, we demonstrate that the mechanisms specifying neuronal diversity also govern circuit formation and function, and that these principles are broadly applicable throughout the nervous system. 

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5. Dopamine-Dependent Plasticity Is Heterogeneously Expressed by Presynaptic Calcium Activity across Individual Boutons of the Drosophila Mushroom Body

   https://doi.org/10.1523/ENEURO.0275-23.2023  

   Davidson, Andrew M.; Kaushik, Shivam; Hige, Toshihide (October 2023, eneuro)

   Abstract TheDrosophilamushroom body (MB) is an important model system for studying the synaptic mechanisms of associative learning. In this system, coincidence of odor-evoked calcium influx and dopaminergic input in the presynaptic terminals of Kenyon cells (KCs), the principal neurons of the MB, triggers long-term depression (LTD), which plays a critical role in olfactory learning. However, it is controversial whether such synaptic plasticity is accompanied by a corresponding decrease in odor-evoked calcium activity in the KC presynaptic terminals. Here, we address this question by inducing LTD by pairing odor presentation with optogenetic activation of dopaminergic neurons (DANs). This allows us to rigorously compare the changes at the presynaptic and postsynaptic sites in the same conditions. By imaging presynaptic acetylcholine release in the condition where LTD is reliably observed in the postsynaptic calcium signals, we show that neurotransmitter release from KCs is depressed selectively in the MB compartments innervated by activated DANs, demonstrating the presynaptic nature of LTD. However, total odor-evoked calcium activity of the KC axon bundles does not show concurrent depression. We further conduct calcium imaging in individual presynaptic boutons and uncover the highly heterogeneous nature of calcium plasticity. Namely, only a subset of boutons, which are strongly activated by associated odors, undergo calcium activity depression, while weakly responding boutons show potentiation. Thus, our results suggest an unexpected nonlinear relationship between presynaptic calcium influx and the results of plasticity, challenging the simple view of cooperative actions of presynaptic calcium and dopaminergic input. 

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