Biology subjects

Jun, E. J.

Publications and source records attributed to Jun, E. J..

5 recordsLinked to original sources

bioRxiv2026

The curse of dimensionality in motor cortex

Understanding how motor cortex generates movement is a foundational challenge in neuroscience. Unsupervised dimensionality reduction techniques, such as principal component analysis (PCA), are widely used to transform high-dimensional neural recordings into a compact, low-dimensional space. The dimensionality of this space--that is, the number of principal components needed to explain a fixed fraction of variance--is broadly assumed to be an intrinsic property of the underlying neural dynamics, potentially modulated by task complexity. Here, by comparing con-strained reaching and unconstrained naturalistic behaviors recorded from the same animal on the same day, we show that this assumption breaks down in two distinct ways. First, across four non-human primates, the dominant axes of low-dimensional neural activity separate behavioral contexts rather than movement kinematics, with neural activity shifting rapidly between task-specific regions of state space at task transitions. Notably, traditional dimensionality metrics are insensitive to movement complexity across tasks. Instead, unsupervised dimensionality scales with the number of recorded neurons, exhibiting non-saturating growth up to 1000 simultaneously recorded electrodes, a pattern that holds across PCA, factor analysis, shared variance component analysis, and nonlinear autoencoders. This scaling has direct consequences for decoding: while decoders trained on unsupervised subspaces improve only modestly with electrode count, super-vised methods leverage additional electrodes to separate neural states from a vanishingly small fraction of total variance (<10% at 1000 electrodes). Together, these results challenge current views on cortical dimensionality, reveal a greater-than-appreciated role for behavioral context in shaping motor cortical activity, and motivate careful consideration of computational methods as experimental data volumes scale.

neuroscience↗

bioRxiv2026

Neural modes in motor cortex cycle over fast timescales

The prevailing opinion in systems neuroscience is that motor cortex generates consistent behavior through a stable neural manifold--a low-dimensional mapping from neuron population activity to kinematics. However, standard population analyses group many repeated trials to reduce estimation noise, obscuring the time-varying activity of the network. Here, a block-by-block analysis of task trials in two species revealed that motor cortex rotates its principal subspaces as the contribution of individual neurons fluctuates, maintaining stable dynamics that are coupled to the neural state. While static decoders performed inconsistently due to non-stationary neuron activity, we confirmed that decoding performance could be rescued through subspace alignment, finding that roughly half of this geometric correction was driven by the internal rank-swapping of dominant state eigenvectors. Rather than relying on a static mapping to execute reaching behavior, motor cortex maintains a library of redundant state eigenvectors that generalize over different reach directions. Model simulations demonstrated that strong excitatory coupling combined with spike-rate adaptation is sufficient to produce a latent library whose elements can swap rank during continuous reparameterization of the network state. Together, these results refine our understanding of motor control: stable neural manifolds drift and jump within bounded limits, continuously outrunning neuron fatigue during repetitive activation.

neuroscience↗

bioRxiv2025

Context-dependent low-dimensional neural dynamics unfold in distinct subspaces, dimensionality, and dynamical strength for natural walking and reaching

Awake behaving animal experiments paired with multichannel electrode recordings have advanced motor systems neuroscience in creating models of how the mammalian brain controls move-ments. However, growing theoretical and experimental evidence question the generalizability of such findings from constrained studies to ambulatory behavior, highlighting a limitation in our understanding of how the brain controls movement. To address this question, spiking neural activity during highly-practiced, routine movement (walking) and goal-directed behavior (reach-ing towards food) were compared in an unconstrained setting. Kinematic trajectories of the contralateral arm during reaching and walking were statistically similar, as were the average single-neuron firing rates during these respective movements. However, the dimensionality of reaching was higher than that of walking and existed in largely non-overlapping subspaces. Further, when modeled as dynamical systems, reaching decayed 3-5 times more quickly than walking. Taken together, these findings demonstrate that the low-dimensional structure of motor cortex is more complex for goal-directed reaching than in highly-practiced natural movements. Since this difference is primarily observable at the state and dynamical systems level, these findings suggest behavioral context plays a significant role in the coordination of otherwise kinematically similar movements, providing indirect evidence for non-cortical circuits such as central pattern generators.

neuroscience↗

bioRxiv2022

Direct comparison of epifluorescence and immunostaining for assessing viral mediated gene expression in the primate brain

Viral vector technologies are commonly used in neuroscience research to understand and manipulate neural circuits, but successful applications of these technologies in non-human primate models have been inconsistent. An essential component to improve these technologies is an impartial and accurate assessment of the effectiveness of different viral constructs in the primate brain. We tested a diverse array of viral vectors delivered to the brain and extraocular muscles of macaques and compared three methods for histological assessment of viral-mediated fluorescent transgene expression: epifluorescence (Epi), immunofluorescence (IF), and immunohistochemistry (IHC). Importantly, IF and IHC identified a greater number of transduced neurons compared to Epi. Furthermore, IF and IHC reliably provided enhanced visualization of transgene in most cellular compartments (i.e., dendritic, axonal, and terminal fields), whereas the degree of labeling provided by Epi was inconsistent and predominantly restricted to somas and apical dendrites. Because Epi signals are unamplified (in contrast to IF and IHC), Epi likely provides a more veridical assessment for the amount of accumulated transgene and, thus, the potential to chemo- or optogenetically manipulate neuronal activity. The comparatively weak Epi signals suggest that the current generations of viral constructs, regardless of delivered transgene, are not optimized for primates. This reinforces an emerging viewpoint that viral vectors tailored for the primate brain are necessary for basic research and human gene therapy.

neuroscience↗

bioRxiv2020

Embodied Cognition and Decision-Making in the Primate Superior Colliculus

A popular model of decision-making suggests that in primates, including humans, decisions evolve within forebrain structures responsible for preparing voluntary actions; a concert referred to as embodied cognition. Embodied cognition posits that in decision tasks, neuronal activity generally associated with preparing an action, actually reflects the accumulation of evidence for a particular decision. Testing the embodied cognition model causally is challenging because dissociating the evolution of a decision from preparing a motor act is difficult, if the same neuronal activity instantiates both processes. Ideally, one would show that manipulation of neuronal activity thought to be involved in movement preparation actually alters decisions, and not movement preparation. Here, trained monkeys performed a two-choice perceptual decision-making task in which they judged the orientation of a dynamic Glass pattern before and after unilateral, reversible inactivation of a brainstem area involved in preparing eye movements, the superior colliculus (SC). Surprisingly, we found that unilateral SC inactivation produced significant decision biases and changes in reaction times consistent with a role for the SC in evidence accumulation. Fitting signal detection theory and sequential sampling models (drift-diffusion and urgency-gating) to the data revealed that SC inactivation produced a decrease in the relative evidence for contralateral decisions. Control experiments showed that SC inactivation did not result in eye movement biases ruling out interpretations based on motor preparation or spatial attentional impairment. The results provide causal evidence for an embodied cognition model of perceptual decision-making and provide compelling evidence that the SC of primates plays a causal role in how evidence is accumulated for perceptual decisions, a process that is usually attributed to the cerebral cortex.

neuroscience↗